The Science of Existence – Metabolism


All cells have the ability to sense whether nutrients are scarce or abundant so that appropriate anabolic or catabolic programs can be initiated. ~ Norwegian cytologists Hilde Abrahamsen & Harald Stenmark

Metabolism comprises the cellular chemical reactions that provide energy to sustain life. The mitochondria in eukaryotic cells are the site of respiratory metabolism. Via metabolism, organisms grow, maintain themselves, ecologically interact, and reproduce.

Metabolism is sometimes defined more expansively, for an organism rather than at the cellular level, thus including digestion and the transport of substances between cells. By this broader definition, metabolic cellular processes are more specifically called catabolism.

Catabolism is the controlled cellular process of breaking down organic matter to harvest energy via cellular respiration. During catabolism, polymers are reduced to monomers. Polysaccharides are broken down into monosaccharides; lipids into fatty acids; nucleic acids into nucleotides; and proteins into amino acids. Cells use resultant monomers either for energy, by further breakdown, or to construct new polymers, via anabolism.


Cellular metabolism is driven by redox reactions: oxidation of one molecule and reduction of another. Redox is a portmanteau for reduction-oxidation: a chemical species having its oxidation state changed. Reduction is a gain of electrons, or a decrease in oxidation state by a molecule, atom, or ion. Oxidation is an increase in oxidation state via loss of electrons.

Reduction potential is the tendency of a chemical species to acquire electrons, and thereby be reduced. A reductant is a chemical species that donates an electron to another species. Hydrogen (H), with an oxidation state of +1, is the strongest reductant, as it freely gives its sole electron for chemical reactions.

Oxidation state, also termed oxidation number, refers to an element’s bonding potential in a reaction when the element is in a molecule. Thus, oxidation state characterizes the charge potential of an atomic species within a compound. Oxidation number is expressed as an integer.

Carbon (C) has an oxidation state of –4. H = +1, while H2 = 0, as H2 is a stable monoatomic molecule comprising only hydrogen. Hence, H2 has no oxidation potential.

Similarly, oxygen (O) = –2, while O2 = 0. Hence, O2 has no reduction potential.

Figuring oxidation state can be tricky. The oxidation number of oxygen in H2O = –2, but in peroxides, such as hydrogen peroxide (H2O2), oxygen’s oxidation state = –1.

As H2O2 is an electrically neutral compound, the sum of the oxidation states must = 0. Since each hydrogen atom has an oxidation number = +1, and hydrogen is more electropositive than oxygen is electronegative, to balance the oxidation number of H2O2 to zero, each O atom must have an oxidation state = –1.

An electrically neutral compound necessarily has a net oxidation state of zero. In figuring oxidation number, a more electronegative or electropositive element trumps a lesser one.

Fluorine (F), with an oxidation number = –1, is the most electronegative element, and so a strong oxidant. In fluorine monoxide (F2O), the fluorine is more electronegative than oxygen, so balancing the oxidation state of this neutral compound requires that oxygen has an oxidation state = +2.

To summarize, redox is a change during a reaction that involves loss or gain of electrons, with reduction a gain and oxidation a loss.

Electron Transport Chains

Electron transfer is the elemental transaction in chemical reactions. An atom donates an electron to another atom in a process that takes a few quadrillionths (10-15) of a second.

An electron transport chain comprises electron transfer between a series of electron donors and acceptors. Electron transport chains are formed by protein complexes embedded in a membrane that act concertedly during a sequence of redox reactions.

A complex is reduced by accepting electrons. Conversely, a complex is oxidized when it gives up electrons.

An electron transport chain works because each acceptor, the next in the chain, is more electronegative than the donor. For an electron transport chain to function – allowing electrons to pass through – an exogenous electron acceptor must be present at the end of the chain.

Some protein complexes use electron transport chains to transfer H+ ions (protons) across a membrane. This is part of the oxidative phosphorylation process, which is a metabolic pathway to use energy released by the oxidation of nutrients to produce ATP.


The simple sugar glucose can be metabolized to release some energy and store the rest as ATP (adenosine triphosphate). ATP is the universal energy currency of life. All cells store surplus energy as ATP, which acts like a rechargeable battery for cellular energy.

Chemical energy transport within cells transpires by shuttling ATP. Cells use ATP not only for energy but also for communication within and between cells – a cellular coin of the realm.

In releasing energy to a cell, ATP turns into ADP (adenosine diphosphate). In storing energy for later use, ADP becomes ATP.

ATP is a nucleotide, comprising 3 main structures: a nitrogenous base (adenine); a sugar (ribose); and a chain of 3 phosphate groups (triphosphate), bound to the ribose.

The adenine ring and ribose sugar form adenosine, which is a purine nucleoside. In animals, adenosine acts as a neuromodulator, promoting sleep and suppressing arousal. On its own, adenine (A) is a nucleobase.

Nucleobases (nucleic acid bases) are nitrogen-based, ring-shaped molecules that comprise the cornerstones of nucleotides. Nucleobases comprise the individual units of the nucleic acids DNA and RNA.

The active part of ATP is the triphosphate. The 3 phosphorous groups are connected to each other by oxygen atoms, with side oxygens connected to the phosphorous atoms.

ATP is formed by adding a 3rd phosphate group to ADP, turning the diphosphate (ADP) into a triphosphate (ATP).

When extra energy is available – from food (in animals) or sunshine (in plants) – ADP is charged into ATP via glycolysis: an energy reservoir to provide a source of power when needed. Photosynthesizers power photophosphorylation from the energy of sunlight. Otherwise, via the internally powered redox of cellular respiration, cells turn ADP into ATP. Generally, ATP production has an energy efficiency of ~54%, well above that of the most efficient machines.

Energy can be gained from ATP by dephosphorylation: ditching at least 1 phosphate group via hydrolysis, turning ATP into ADP. The negatively charged side oxygen atoms in phosphate are uneasy in proximity and would like to escape the association; the escaping oxygen atom dragging its attached phosphate with it.

An ATP molecule would be content with just 2 phosphate groups instead of the 3 that it is saddled with. ATP (triphosphate) is just itching to become ADP (diphosphate).

ATP + H2O → ADP + Pi

Via hydrolysis, the easily triggered conversion of ATP into ADP releases energy that cells use to power themselves. Hydrolysis is the process of splitting H2O into H+ and OH; a redox reaction that creates usable energy. Conversely, when extra energy is available – from food (in animals) or sunshine (in plants) – ADP is charged into ATP via glycolysis, stocking a reserve to provide power when needed.


Cellular respiration comprises the metabolic processes that convert nutrients into ATP. The many individual reactions of respiration are catabolic reactions involving redox. A cell gains useful energy via respiration.

Respiration relies upon an electron transport chain. Molecular oxygen is a highly oxidizing agent, and so is an excellent electron acceptor. Both aerobic and anaerobic respiration involve the transport of hydrogen ions (H+) or electrons to oxygen, which is then reduced.

Aerobic respiration has the advantage of oxygen as an input to the respiration process, thus affording the complete breakdown of a glucose molecule via glycolysis, a metabolic pathway. Hence aerobic respiration oxidizes glucose (C6H12O6) to carbon dioxide (CO2), and reduces oxygen (O2) to water (H2O).

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O

Oxidizing 1 molecule of glucose via aerobic respiration produces 2.28 attojoules of energy.

Prokaryotes arose before atmospheric oxygen was readily available, and so had to make do with anaerobic respiration. Many anaerobic organisms are obligate anaerobes: they can respire only using anaerobic compounds. Oxygen is deadly to them.

Anaerobic respiration is respiration using a substitute electron acceptor rather than oxygen in the initial stages. Anaerobic glycolysis incompletely breaks down glucose, yielding ethyl alcohol (C2H5OH) and carbon dioxide.

C6H12O6 → 2 C2H5OH + 2 CO2

Anaerobic respiration is much less energetically efficient than aerobic respiration. With smaller reduction potential, 9 times less energy is released per glucose molecule: 0.25 attojoules.

Eukaryotic tissues resort to anaerobic respiration when deprived of oxygen. Anaerobic glycolysis results in the lactate that appears in overworked muscles.


In being largely hydrocarbons, lipids are more complex in their metabolic redox than sugars. Energy from fat is not as easily released as it is from carbohydrates.

From a redox point of view, whereas plants are sun-powered, animal metabolism is driven by inhaled oxygen added to migrating food electrons.


Biosynthesis is the cellular construction process: converting substrates into more complex products. In this context, a substrate is the material upon which enzymes act to create a bioproduct. Common biosynthetic products include carbohydrates, proteins, vitamins, and lipids.

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Biosynthesis and anabolism seem to be synonyms. Conceptually they are, but anabolism is most often used to refer to metabolic pathways: series of chemical reactions within a cell.

Metabolic Pathways

The organization of cooperating enzymes into macromolecular complexes is a central feature of cellular metabolism. A major advantage of such spatial organization is the transfer of biosynthetic intermediates between catalytic sites without diffusion into the bulk phase of the cell. ~ American biochemist Brenda Winkel

A metabolic pathway is a series of chemical reactions occurring within a cell, commonly with an intended biological end product, along with inevitable waste. Metabolic rate is the speed at which a pathway transpires.

A metabolic pathway modifies an initial molecule (substrate) into a product, which may be used in 1 of 3 ways: 1) immediately, as an end product; 2) intermediately: to initiate another metabolic pathway (a flux-generating step); or 3) stored by the cell for later.

Metabolic pathways are either productive (anabolic) or degradative (catabolic). Catabolism breaks matter down, anabolism builds it up. Anabolism is sometimes referred to as constructive metabolism; catabolism as destructive metabolism.

There are as many metabolic pathways as there are products, both catabolic and anabolic. Metabolic pathways are highly organized highways within cells, affording efficient channeling and construction of substrates into products. Efficacy in catabolic processing is abetted by limiting diffusion of intermediate products, thus keeping requisite chemical stocks in readily available pipelines.

Though there are several hundred pathways for any cell, only a couple dozen are critical to cell functioning. These critical pathways are identical in most forms of life – a package which has been conserved through evolutionary time.