The Science of Existence – Molecules


A molecule is a bonded conglomeration of atoms in tentative relationships. 37 distinct types of chemical reactions are known.

When atoms and molecules undergo chemical reactions, the electrons are the ones that do the heavy lifting. They regroup and move to allow new bonds between molecules to be created or destroyed. ~ Swedish atomic physicist Marcus Isinger

Empedocles considered chemical changes as emotional relations: substances combine in love to birth something new, or discordantly divorce. No wonder it’s called chemistry.

“Nature does what must be done to achieve equilibrium, which is a minimum-energy configurational space.” ~ American chemist Scott Chambers


Atoms join into molecules by sharing electron bonds. In becoming a molecule, atoms give or take electrons, depending upon their species. Atoms with few electrons in their outermost shell are (electron) donors, while those in want of a few are acceptors.

In forming molecules, atoms tend to find the most stable relationships among themselves. This takes the form of bonding that requires the least energy to sustain the association.

Without its outer shell of electrons filled to the brim, an atom feels lonely, and readily mingles with another. The mingling may be inscrutable.

Glass seems solid, but at the molecular level, glass resembles a liquid. Its molecules do not make a tidy lattice, like crystals do. Instead, glass is a molecular jumble. How glass settles into its dual state – solid with a liquid structure – is a mystery.


Each electron shell of an atom has a limited capacity. The 1st shell layer (shell 1) is stable at 2 electrons. The 2-electron atom helium (He) is relatively stable, and so reluctant to join with other atoms to make a molecule.


Helium’s lightweight cousin, hydrogen (H), is the most abundant chemical element, and the simplest. With only 1 electron, hydrogen is a randy joiner: willing to donate its electron to make a molecule. Hydrogen’s enthusiasm plays an indelible importance in cosmic construction, and in the dynamics of life.

The simplest molecule is diatomic hydrogen gas (H2), which creates a closed shell configuration with 2 electrons. Diatomic refers to 2 nuclides of the same type of atom (atomic species) forming a molecule. Most diatomic molecules are gases. Hence H2, O2, and N2 are molecularly happy campers, mated with each other.

Normally, hydrogen is a gas of diatomic molecules. Pressure and temperature can change the situation. When cooled enough, hydrogen solidifies. Compressed hydrogen has 3 phases as a quantum crystal, consisting of rotating molecules in tightly packed hexagonal lattices.

Another phase appears at 2.2–3.4 million times normal atmospheric pressure, with 2 divergent types of hydrogen molecules in its structure. One type interacts very weakly with its neighbors, which is unusual for molecules under high compression. The other type of molecule tightly bonds with its neighbors, forming planar sheets. Solid hydrogen under these conditions is on the borderline between a semiconductor, like silicon, and a semimetal, like graphite.

At tens of millions times pressure, hydrogen turns into a metal. The interior of Jupiter is largely cold, metallic hydrogen; some of it as a liquid metal.

With hydrogen, nothing is simple. ~ condensed matter physicist Eugene Gregoryanz


The 1st shell of an atom, as with helium, has only 2 electrons. The 2nd shell is full at 8 electrons. Since negatively charged electrons are attracted to their positively charged nucleus, electrons in an atom will generally occupy an outermost shell only when the shells within have been filled.

The general formula for filling shells is 2 x 2n, where n is the shell number. Hence: 2 = 2 x 12; 8 = 2 x 22; 18 = 2 x 32; 32 = 2 x 42.

Atoms with an incomplete outer shell naturally bond with other atoms to form molecules. These bonds involve sharing electrons.

The valence of an atom tells how many electrons an atom needs to fill its outermost shell. The chemical properties of an atom are defined by its outermost shell: the valence shell.

The simple story is that the valence shell determines how reactive an atom is. More accurately, the electrons traveling farthest from the nucleus – the most energetic ones – determine how an atom reacts chemically. These valence electrons are necessarily in the valence shell.

Oxygen, at 2|6, has a valence of 2, and so readily combines with 2 atoms of hydrogen gas to make H2O: water (6 (from oxygen) + 2 (from hydrogen) = 8 (stable valence shell)).

The 5 most abundant elements in the solar system are: hydrogen (1), helium (2), oxygen (2|6), carbon (2|4), and nitrogen (2|5). Only helium is not prone to forming molecules.

Helium is rare on Earth and has no role in organic chemistry. The other abundant atomic species – carbon, nitrogen, oxygen, and hydrogen – all play active roles in organic chemistry precisely because they are reactive.

Covalent Bonds

In forming molecules, electron shells fill themselves out by sharing pairs of electrons. This is basic chemical affinity: forging a covalent bond, with electrons portioning their orbits among atoms.

There are several types of covalent bonds, which vary by the nature of electron sharing. Sigma, pi, and 3-center 2-electron bonds are illustrative.

A sigma bond (σ) is the strongest type of covalent bond, corresponding to valence shell sharing as previously described.

A pi bond (π) is formed by overlapping atomic orbital lobes. Pi bonds are more diffuse than sigma bonds, and so somewhat weaker.

In a >3-center 2-electron bond (3c-2e), 3 atoms share 2 electrons. This odd bonding comes up an electron short. Typically, the bonding orbital is not equally allocated, but skewed toward 2 of the 3 atoms in the molecule. The simplest example of 3c-2e bonding is H3+: the trihydrogen cation.

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Covalent bonding takes energy. The strength of a chemical bond – bond energy – is measured by the energy needed to separate the bonded atoms of a molecule.

Electronegativity is electron sex appeal: the ability of an atom or molecule to attract electrons. Electronegativity is an inelegant term, and confusing, because it applies to the positive appeal that an element has for an electron, albeit an electron is negatively charged.

On the other end of the electron exchange program, some elements are willing to donate electrons. The measure of electron donation willingness is termed electropositivity.

 Bond Orders

A covalent bond may be of a single, double, or triple electron pair. Quintuple bonds exist, but are rare, confined to certain metals. A quintuple bond involves 10 electrons bonding between 2 metal centers.

Diatomic fluorine (F2) is an exemplary single bond. Molecular oxygen (O2) is cozy as a double bond, while molecular nitrogen (N2) forms a triple bond.

The higher the bond order, the tighter the bond – literally: bond length shortens. Bond energy increases with bond order. Tighter bonds are energetically stronger. Hence, the triple bond of dinitrogen is a particularly strong one.

Ionic Bonds

Electrostatic attraction results in 2 oppositely charged ions coupling. This is ionic bonding.

Ionic bonds are formed between a cation and an anion. A cation is an ion with a positive charge, as it has fewer electrons than protons. Conversely, an anion has a surfeit of electrons, and so is negatively charged. A cation is commonly a metal, while the average anion is a nonmetal.

All ionic compounds also have some degree of covalent bonding. The larger the electronegativity between the atoms involved in bonding, the more ionic (polar) the bonding is.

Ionic molecules are electrically conductive when molten or in solution but not when they are a solid. Ionic compounds tend to be water-soluble and have a high melting point.

While compounds with ionic bonds intact are electrically neutral, they are subject to ionization upon encountering a solvent: the partner atoms disassociate back into ions. Electrolytes are substances, such as salts, acids, and bases, that release ions when dissolved in water.

Hydrogen Bonds

A hydrogen bond is the attraction between a hydrogen atom and an electronegative atom, such as oxygen, nitrogen, or fluorine. Hydrogen bonds may be within a single molecule or between molecules.

A hydrogen bond is weaker than a covalent or ionic bond, but stronger than the van der Waals interaction, which couples 2 dipoles via HD connection.

Commonly, hydrogen bonds form between the ends of polar molecules. Water molecules attain their fluidity through hydrogen bonds. The high boiling point of water (100 °C) owes to intermolecular hydrogen bonding, as does water’s surface tension.

Hydrogen bonds hold the 2 halves of DNA together. Hydrogen bonds facilitate the complex 3d structures that proteins take. More generally, hydrogen bonding plays an important role in the structure of polymers.

Bonds Beyond

There is a standard law that says as you lower the temperature, the rates of reactions should slow down. ~ English chemist Dwayne Heard

The vast expanse of interstellar space is supposed to be too cold for most chemical reactions to occur. The more frigid it gets, the harder it is to spark a chemical reaction for lack of energy, which is the very definition of cold.

Yet a vast variety of complex organic molecules are formed in space. Some reactions transpire on the surface of cosmic dust grains, or with a little help from gamma rays or stray high-energy electrons. But most happen beyond the laws of chemistry.

Colossal clouds of alcohol float in Sagittarius B2: a giant molecular basin of gas and dust, 120 parsecs from the center of the Milky Way. These clouds are at a balmy 40 K or less: far too cold to explain such ample booze in space. Interstellar spirits brew despite chemistry’s cardinal rules giving them the cold shoulder. They do so by quantum tunneling, which is an hd trick that allows a particle to surmount a barrier that it cannot breach classically.

“The tunneling of a particle through a potential barrier is a key feature of quantum mechanics that goes to the core of wave–particle duality. The phenomenon has no counterpart in classical physics. Tunneling events are only as ‘instantaneous’ as the electron wavefunction collapse that orthodox interpretations of quantum mechanics associate with the appearance of continuum electrons. (Continuum mechanics is the study of matter as a process.” ~ Russian physicist Igor Litvinyuk et al

The label quantum tunneling names, but does not explain, one of Nature’s most mysterious mechanisms. Despite the intense energy already invested, nuclear fusion nevertheless depends upon quantum tunneling.

The method for making methoxy comes in combining methanol gas with a hydroxyl radical. Both are found in the cold expanse of space, but the energy to put the two together is not. Nonetheless, reactions happen, and prodigiously so. Quantum tunneling bestirs interstellar spirits 50 times faster than would occur sitting at room temperature.

There is organic chemistry in space of the type of reactions where it was assumed these just wouldn’t happen. Scientists have been severely underestimating the rates of formation and destruction of complex molecules, such as alcohols, in space. ~ Dwayne Heard

HD Harmonically Bound

Bonding can also occur by the non-conservative forces responsible for interaction-induced coherent population trapping. The bound state arises in a dissipative process and manifests itself as a stationary state at a preordained interatomic distance. Remarkably, such a dissipative bonding is present even when the interactions among the atoms are purely repulsive. ~ Russian physicist Mikhail Lemeshko & German quantum physicist Hendrik Weimer

A bond between atoms typically forms when it is energetically more favorable for atoms to stick together than stay apart. This requires an attractive force.

Even energetic repulsion between atoms can be overcome by local HD harmonic fluctuations of the ground state, which generate a quantum interference that nullifies repulsion, trapping atoms into union at a distance which sets the bond length.

The nature of an HD harmonic bond is strikingly different than ordinary chemical bonds, most notably in being remarkably robust. Even applying a constant amount of energy may not break a harmonic bond.

Molecular Geometry

“Shape is destiny in the world of molecules.” ~ American philosopher Daniel Dennett

The position of each atom in a molecule is determined by the nature of bonding with its neighbors. Molecular geometry is determined by the quantum behaviors of atomically bound electrons. Molecular geometry characterizes the shape of molecules by the positions of constituent atoms in space – evoking the bond length between 2 atoms, the bond angles among 3 atoms across 2 bonds, and the torsional angle of atoms chained together, such as carbon chains.

Torsional angle is the angle between 2 planes. In molecular geometry, bonded atoms in a chain form 1 or more planes.

Molecules form a tremendous variety of 3D shapes. The geometry of a molecule affects and reflects its reactivity, polarity, phase, color, magnetism, and biological activity.

Isomers are compounds with the same molecular formula but different shapes. As molecular structure is functionally significant, isomers may have different properties than their cousins with the same atomic composition.

Each molecular bond is a region of negatively charged electrons. These regions repel each other. Individual bonds want to stay as far away from others as possible.

Molecules assume a geometry that minimizes the repulsive energies of electron orbital regions. These regions always include shared electron pairs between atoms in a molecule, but valence shell electrons that stay at home also get into the act.

“Most of the modern understanding of chemistry, including the very notion of a well-defined molecular structure, rests on the concept of a potential energy surface – a 3N-dimensional ‘landscape’ that plots the total energy of a collection of N atoms as a function of the atomic positions.” ~ American chemist Todd Martinez

Lone Pairs

The electrons in the valence shell of an atom in a molecule may not be shared. A nonbonding valence electron pair is termed a lone pair.

Lone pairs fashion a high electron density in their region of orbital space. So, even though they are not bonded, lone pairs influence the shape of a molecule.

In bonding, shared electrons are concentrated between 2 atoms. Lone pairs, without the attention of a 2nd atom, are cozy homebodies: typically located a bit closer to the atomic nucleus than bonding pairs.

Lone pairs often exhibit a negative polar character. As electron regions repel each other, a lone pair nudges its brethren bonding pair away, reducing molecular bond angle.


When atoms with different electronegativity join by covalent bonding, electrons may not be equally shared: electrons are pulled more toward one atom than another. When this happens, the force of alignment causes one end of a molecule to have an overall negative charge, leaving the other end to assume a positive charge. A molecule with such an unequal charge distribution is polar.

Polarity means that a molecule has positive and negative poles; in other words, the molecule possesses an electric dipole moment. Polarity underlies several physical properties, including surface tension, solubility, and critical thermodynamic points (melting and boiling). Water (H2O) is the poster child of polar molecules.

Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds. A polar molecule with multiple polar bonds must have an asymmetric geometry so that the bond dipoles do not cancel each other.

Nonpolar molecules share electrons equally, rendering them electrically neutral. Oxygen (O2) and methane (CH4) are nonpolar, as are lipids: fat not being so easily excited makes it a relatively contented energy storage medium.


While all matter is characterized by mass, a gas has only mass. A liquid has, in addition, a specifiable volume. A solid has, besides mass and volume, some specific shape. ~ Steven Vogel

The states of matter may be positively classified in various ways. Gases and liquids are fluids, whereas crystals and glasses are solids. Alternate views emphasize density or atomic arrangement.

Gases naturally expand to occupy available volume. A plasma is an ionized gas. Liquids maintain their volume but adapt their shape when confined. Solids maintain their volume and shape.

99% of the matter in the universe is plasma, including stars and the medium that permeates in between. Most plasmas are in a turbulent state, threaded with magnetic fields that generate magnetic reconnection.

A crystal is characterized by an orderly, repeating 3d pattern. A lattice is a typical crystal.

In contrast, glass has an amorphous structure that undergoes a glass transition while being heated toward a liquid state. The glass transition temperature is always lower than the melting temperature.

The glass transition of a liquid toward a solid may be inspired by cooling or compression. This transition is a smooth increase in viscosity, by as much as 17 orders of magnitude before any pronounced change in structure.

Triple Point

At any temperature and pressure, the thermodynamically stable phase of a compound is the one with the lowest free energy – that is, compounds are most stable when then have acquired the maximal amount of local energy. The arrangement, motion, and interactions among chemical constituents determines this.

When 2 phases coexist stably, their free energies must be equal. This condition forms a coexistence line in a phase diagram.

Ice and water coexist in equilibrium at 0 °C and atmospheric pressure. Increasing pressure decreases melting point.

Similarly, water vapor and liquid coexist stably at 100 °C and atmospheric pressure. Decreasing pressure drops that temperature. Hence water boils at a lower temperature on top of a mountain than at sea level.

These 2 coexistence curves can only intersect at a single value of temperature and pressure. The triple point is the temperature and pressure at which a specific molecular structure coexists in the 3 phases: gas, liquid, and solid.

The singular stability of water – where water is simultaneously vapor, liquid, and ice – is at 273.16 K (0.01 °C) and 611.73 pascals. This particular triple point defines the Kelvin temperature scale. From its triple point, slight changes in pressure and/or temperature transforms water alternately to ice, liquid, or vapor.

The triple point of H2O is also the minimum pressure at which water is liquid. At pressures below the triple point, such as in outer space, a rise in temperature (at constant pressure) turns ice into vapor; a process termed sublimation. A temperature rise at constant pressure above triple point melts ice to liquid.

Water is peculiar in many ways, including its triple point behavior. Whereas the melting point of ice to liquid water decreases as a function of pressure, for most substances, the triple point is the minimum temperature at which a liquid can exist. For water, at a constant temperature just below the triple point, compression turns water vapor to ice, then to liquid form.

In addition to phase transition, for solid polymorphs – materials that may exist in different forms – there can be multiple solid triple points. Helium-4 is a unique polymorph in having a triple point for 2 different fluid phases (known as its lambda point).


The internal coherence of a liquid makes a surface something unattractive which the system will arrange itself to minimize. A droplet will spontaneously round up into a sphere. ~ Steven Vogel

Although the surfaces of liquids and crystals differ, they both have a tendency toward minimizing surface area. This owes to the energy associated with such a boundary.

A surface atom lacks neighbors on one side and so has a deficit of interatomic bonds. Bond energies are negative, so the missing surface bonds correspond to a positive energy contribution.

For a crystal, surface tension arises from stretching interatomic bonds, whereas liquid surface tension is more about the extra atoms introduced when spreading out in increased surface area.

Interesting dynamics transpire at the interface of different substances. Cocktails come with complete miscibility: a thorough water-alcohol mixture. This passage of molecules between species is known as diffusion.

If instead the interphase bonding is competitive, the liquid wets the solid. Solders and brazes function as they do by readily wetting metallic surfaces.

Water is especially sensitive to its environment: reacting distinctly depending on what it interfaces with. This reactive versatility is called wettability: spreading when a material is wettable or beading when not. Wetting occurs when the adhesion of liquid to solid gains the advantage over internal cohesion.

Mercury (Hg) does not wet glass. Hence its meniscus (surface) in a thermometer is concave: bulging upward, lower along the edges.

In contrast, water wets glass, owing to the attraction of H2O to the silica in glass. Hence water in a glass is convex: bulging downward, higher at the edges.

Capillary action – the ability of a liquid to readily flow when narrowly confined in a solid tube, essentially ignoring gravity – owes to wetting. Vascular plants are major employers of capillary action.


Helium is the 2nd lightest and 2nd most abundant element, right behind hydrogen. The two could not be more different. Helium’s stability is the opposite of hydrogen’s volatility.

Helium is a gas except under extreme conditions. Helium has the lowest boiling and melting points. Helium becomes a liquid at 4.2 K. Below 4 K, helium fiercely boils.

Below 2.172 K, the boiling stops; helium becomes a superfluid. A superfluid exhibits zero viscosity and zero entropy. Superfluid helium flows without friction; through tiny holes as small as a molecule, up and out of a tube, over the edge of a cup.

More particularly, helium-4, the ubiquitous isotope comprising 2 neutrons with 2 protons, becomes a superfluid more readily than helium-3, which is a rare isotope, with only 1 neutron per helium atom. Helium-3 only becomes a superfluid when chilled to 2 millikelvins.

The reason is that helium-4 atoms are bosons, whereas helium-3 atoms are fermions. Hence helium-4 corresponds to the characteristics of Bose-Einstein condensation, whereas helium-3 becomes a fermionic condensate.

A fermionic condensate interacts by Cooper pairing between atoms, as contrasted to the electron Cooper pairs that facilitate superconductivity.

Helium-4 is bosonic via the subatomic components (protons, neutrons, and electrons) canceling each other’s complementary spins, resulting in zero spin for the helium-4 atom as a whole. This facilitates the stability of helium-4.

Only neon is less reactive than helium, and it needs a cluster of buddies to be so. Neon is most commonly molecular as 20Ne, whereas helium is monoatomic (1He).

Helium is not the only element capable of superfluidity. Rubidium, a highly reactive silvery-white metal, becomes a superfluid at 500 nanokelvins (500 10–9 Kelvin).


Whereas a liquid conforms to its surroundings, a solid rigidly retains its shape. A supersolid is a state of matter that marries solidity with superfluidity.

Like a solid, a supersolid is rigid. Its atoms snap back into place if displaced. But, owing to its highly ordered state, particles can flow through a supersolid without viscosity, aided by quantum mechanics which smear out the positions of quanta being shoved aside.

From the 1950s, theoretical physicists argued whether a supersolid could exist. Failed experiments into the 2110s confirmed doubters. But then in 2016 came experimental proof that supersolids can exist in ultracold quantum matter.

Energy Transitions

The energy of an atom or molecule changes not only when it loses or gains electrons, but also when electron orbits change. It takes energy to move electrons from an inner shell outward. Conversely, some energy is released if electrons move to an inner shell.

The energy to effect shell transitions may be meager. For example, some solids naturally fluctuate between 2 different structural forms, each with a different oscillation frequency. Slight differences at the subatomic level influence the dynamics of transformation.

Intermolecular forces determine temperature magnitude of melting and boiling as well as the solubility of molecules. The greater the attraction between the elements of a specific compound, the higher the melting and boiling points are likely to be.

Nonpolar molecules are most soluble in nonpolar solvents. Likewise, polar molecules are most soluble in polar solvents.

At the molecular level, life transpires as a channeling of energy flows; the chemistry of metabolism. The elements that comprise the mainstay of organic life readily combine in a variety of ways.

As a network of about a thousand enzymatic reactions, metabolism fuels growth by converting nutrients into building blocks and energy. ~ Swiss microbiologist Robert Schuetz

Catalysts & Enzymes

Existence would be much different if chemical reactions transpired at their nominal rate. Instead, Nature quickens the pace with catalysts, which arise in a wide variety of chemical contexts. If not for catalysis, life would not be possible.


Catalysts promote chemical reactions. The term promote is used because it is possible for a reaction to happen without a catalyst, but the likelihood of non-catalytic reaction is analogous to a coin flip resulting in the coin standing on edge: not likely.

Catalysts lower the activation energy required for a reaction to occur. In organic chemistry, that role is played by proteins known as enzymes.


Alcoholic fermentation is an act correlated with life. ~ Louis Pasteur

French chemist and microbiologist Louis Pasteur, thirsty for knowledge, concluded in 1857 that some vital force catalyzed yeast in its fermentation of sugar into alcohol. He termed that vitality ferments. What he discovered were enzymes in action. German physiologist Wilhelm Kühne coined the term enzyme in 1877.

An enzyme is able to speed up a chemical reaction by as much as 10 million times. It had to do this by lowering the energy of activation – the energy of forming the activated complex. It could do this by forming strong bonds with the activated complex, but only weak bonds with the reactants or products. ~ Linus Pauling

An enzyme is commonly defined as a protein that acts as a catalyst in reactions involving proteins or other substrates, typically polymers. A polymer is a large molecule (macromolecule) comprising repeating molecular units (monomers).

Enzymatic action is the karmic wheel of organic life in polymeric construction (anabolism) and deconstruction (catabolism). Enzymes enable the manufacture of macromolecules which may be consumed. Conversely, consumption requires enzymes to break big molecules down to release the energy within.

Because proteins are picky about being prodded to perform, every biochemical reaction is promoted by a specific enzyme.

Every organism contains a vast number of different enzymes, involved in a complex web of metabolic interactions. ~ Andrew Clarke

Enzymes are often quite specific in their binding, but some are also produced to be non-specific, with specificity generated by controlling access to specific substrates – a learning mechanism. Proteins can thus be made to act like switches, by having 2 or more conformations, thus able to interact differently with signaling proteins. This is a facet of intracellular communication.

An enzyme can use a rare and transient conformational state in its substrate to direct an outcome. ~ Canadian geneticist David Pulleyblank

Enzymes dance to do their job. Subtle changes in shape play a crucial role in enzyme function. Enzyme conformational changes are highly dynamic.

2 enzymes with virtually identical molecular shapes may catalyze reactions at very different rates. One may regulate insulin production in humans, while its evil twin gives a bacterium the power of bubonic plague.

The rate of molecular motions is critical to enzyme function. Context matters.

The enzyme responsible for insulin regulation moves slowly, ensuring certainty in cellular processing. Conversely, the plague enzyme is carefree; moving 30 times faster. While proper construction requires meticulousity, the power for destruction can be swiftly rendered.

The exuberance of enzymes often needs to be adjusted to suit cellular needs. The rate of enzymatic activity is affected by a variety of conditions: temperature; ambient chemical environ, such as pH; and chemical concentrations. Whereas activators increase activity rate, inhibitors slow enzymes down. Many drugs and poisons are enzyme inhibitors.

 Humble Agent

The Onion reported a 2013 interview with an α-amylase enzyme involved in speeding up the breakdown of starch into maltose. Calling itself “just a catalyst, nothing more,” the enzyme remarked: “all I did was lower the activation energy required for the reaction to take place, but if I don’t have an amazing substrate to act upon, there is no reaction, period.”

α-amylase commented on all the factors necessary for success. “Say the pH isn’t slightly acidic, or the ions are not properly aligned. Are we left with a simple sugar that can be used as an immediate energy source? Absolutely not. You need teamwork for that, and thankfully, that’s what we had today.”

(The interview was, of course, fictitious. But the point that biochemical reactions are often daedal behaviors is true.)


Every cell produces a significant number of enzymes which appear to be inert. Of the 518 enzymes that are supposed to catalyze proteins involved in phosphorylation – protein kinases – about 10% seem to be duds, as they lack key amino acids to act as catalysts.

The researchers who discovered these pseudoenzymes in 2002 were shocked. “We thought we must have got it wrong,” fumed American geneticist Gerard Manning.

The DNA which delivers dead enzymes are not degraded. Those protein-producing sequences have hardly changed over millions of years.

Instead of catalysts, pseudoenzymes are employed in a variety of other roles. Some help “true” enzymes do their job by shoving them into the correct shape. Some provide a venue where proteins can mingle. Some latch onto receptors to help cells communicate. Some act as bodyguards, escorting another protein to a work site.


The lesson of pseudoenzymes is that there are many other jobs which enzymes do besides catalyzing reactions. A better definition of an enzyme is a protein that facilitates the activities of other proteins or substrates.