Metabolic pathway

In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly. Because of the many chemicals (a.k.a. "metabolites") that may be involved, metabolic pathways can be quite elaborate. In addition, numerous distinct pathways co-exist within a cell. This collection of pathways is called the metabolic network. Pathways are important to the maintenance of homeostasis within an organism. Catabolic (break-down) and Anabolic (synthesis) pathways often work interdependently to create new biomolecules as the final end-products.

A metabolic pathway involves the step-by-step modification of an initial molecule to form another product. The resulting product can be used in one of three ways:

• To be used immediately, as the end-product of a metabolic pathway
• To initiate another metabolic pathway, called a flux generating step
• To be stored by the cell

A molecule called a substrate enters a metabolic pathway depending on the needs of the cell and the availability of the substrate. An increase in concentration of anabolic and catabolic intermediates and/or end-products may influence the metabolic rate for that particular pathway.

Overview

Each metabolic pathway consists of a series of biochemical reactions that are connected by their intermediates: the products of one reaction are the substrates for subsequent reactions, and so on. Metabolic pathways are often considered to flow in one direction. Although all chemical reactions are technically reversible, conditions in the cell are often such that it is thermodynamically more favorable for flux to flow in one direction of a reaction. For example, one pathway may be responsible for the synthesis of a particular amino acid, but the breakdown of that amino acid may occur via a separate and distinct pathway. One example of an exception to this "rule" is the metabolism of glucose. Glycolysis results in the breakdown of glucose, but several reactions in the glycolysis pathway are reversible and participate in the re-synthesis of glucose (gluconeogenesis).

• Glycolysis was the first metabolic pathway discovered:

1. As glucose enters a cell, it is immediately phosphorylated by ATP to glucose 6-phosphate in the irreversible first step.
2. In times of excess lipid or protein energy sources, certain reactions in the glycolysis pathway may run in reverse in order to produce glucose 6-phosphate which is then used for storage as glycogen or starch.

• Metabolic pathways are often regulated by feedback inhibition.
• Some metabolic pathways flow in a 'cycle' wherein each component of the cycle is a substrate for the subsequent reaction in the cycle, such as in the Krebs Cycle (see below).
• Anabolic and catabolic pathways in eukaryotes often occur independently of each other, separated either physically by compartmentalization within organelles or separated biochemically by the requirement of different enzymes and co-factors.

Major metabolic pathways

Glucuronate metabolism

Pentose interconversion

Inositol metabolism

Pentose phosphate pathway

Glycolysis and Gluconeogenesis

Amino sugars metabolism

Small amino acid synthesis

Branched amino acid
synthesis

Purine biosynthesis

Histidine metabolism

Aromatic amino
acid synthesis

Pyruvate
decarboxylation

Fermentation

Fatty acid
metabolism

Urea cycle

Citric acid cycle

Pyrimidine biosynthesis

v · All pathway labels on this image are links, simply click to access the article. A high resolution labeled version of this image is available here.

Cellular respiration

Main article: Cellular respiration

Several distinct but linked metabolic pathways are used by cells to transfer the energy released by breakdown of fuel molecules into ATP and other small molecules used for energy (e.g. GTP, NADPH, FADH).

These pathways occur within all living organisms in some form:

1. Glycolysis
2. Aerobic respiration and/or Anaerobic respiration
3. Citric acid cycle / Krebs cycle
4. Oxidative phosphorylation

Other pathways occurring in (most or) all living organisms include (but are not limited to):

• Fatty acid oxidation (β-oxidation)
• Gluconeogenesis
• Amino acid metabolism
• Urea cycle / Nitrogen metabolism
• Nucleotide metabolism
• Glycogen synthesis / Glycogen storage
• Pentose phosphate pathway (hexose monophosphate shunt)
• Porphyrin synthesis (or heme synthesis) pathway
• Lipogenesis
• HMG-CoA reductase pathway (isoprene prenylation chains, see cholesterol)
• Leloir pathway

Synthesis of energetic compounds from non-living matter:

• Photosynthesis (plants, algae, cyanobacteria)
• Chemosynthesis (some bacteria)

See also

Metabolism portal

• Metabolism
• Metabolic network
• Metabolic network modeling
• Metabolic engineering

External links

• BioCyc: Metabolic network models for hundreds of organisms
• KEGG: Kyoto Encyclopedia of Genes and Genomes
• Reactome, a database of reactions, pathways and biological processes
• MetaCyc: A database of non-redundant, experimentally elucidated metabolic pathways (1800+ pathways from more than 2200 different organisms).
• Metabolism, Cellular Respiration and Photosynthesis - The Virtual Library of Biochemistry and Cell Biology
• PathCase Pathways Database System
• Interactive Flow Chart of the Major Metabolic Pathways
• A novel visualization for a Metabolic Pathway
• DAVID: Visualize genes on pathway maps
• Wikipathways: pathways for the people
• ConsensusPathDB