Powering Bacteria - how do the simplest cells get their energy?
ATP synthase
A model of a mitochondrion, cut-away
Above: the power system of a typical aerobic Gram-negative bacterium such as Escherichia coli. This is a similar process to
aerobic respiration in mitochondria. [The evidence seems incontrovertible that mitochondria evolved from bacteria or
prokaryotes internalised by ancestral cells - mitochondria are evolved bacteria that can no longer live without their host cell
and vice versa.] Organic fuels such as glucose are oxidised in the cytosol (by a complex series of chemical reactions called
glycolysis and Kreb's cycle) removing hydrogen atoms from them. Carrier molecules then transfer these hydrogen atoms to
the inner cell membrane where the
electron transport chain (ETC, shown in orange) strips the electrons from the hydrogen
atoms, generating hydrogen ions (protons, H+).

The energy provided by the electrons flowing through the ETC (as an electric current) is used to pump the protons out across
the inner membrane into the periplasm (situated between the inner and outer membranes). This creates a pool of protons in
the periplasm. When allowed to do so these protons will flow back into the cytoplasm, across the inner membrane, by passive
diffusion down their
electrochemical gradients. [A chemical gradient is a concentration difference, and due to passive
diffusion a chemical moves from a region of high concentration to one of low concentration. An electric gradient is a charge
difference, protons are positively charged and the inside of the cell is negatively charged, and so protons will move into the
cell when allowed to do so since opposite charges attract. The protons will move into the cell down both their chemical and
electrical gradients, and the resulting electrochemical gradient or potential pulls the protons in more strongly than either the
chemical or electrical gradient would acting alone.] The electrochemical gradient results in a force acting on the protons,
driving them to flow, called the
proton-motive force or pmf (a not dissimilar electron-motive force or emf drives electrons
around an electrical circuit and is generated by power cells or batteries, for example).

Specific protein channels in the inner cell membrane allow the protons in the periplasm to re-enter the cell cytoplasm along
their electrochemical gradients. As the protons flow back in, their kinetic energy (due to motion) and also their electrical
energy (current) can be harnessed as a source of energy by the cell. [The kinetic energy of flowing water molecules are
harnessed by a water mill in a similar process, but in this case the cell has a source of kinetic energy and (positive) electrical
energy). Some of these protein channels are transporters.
Importers such as the lactose importer use the energy from one
in-flowing proton to transport each molecule of lactose into the cell. Lactose is a sugar and a useful fuel for the cell. Other
nutrients can be similarly imported, such as amino acids (the building blocks of proteins) like proline. These nutrients are
imported from the periplasm, crossing the outer membrane from the surrounding medium freely by passive diffusion through
large protein pores, called
porins, in the outer membrane. These importers are symporters, because the two particles they
import (a proton and whatever else) travel across the membrane in the same direction. Thus we have a
, and a proline-proton symporter.

Other flowing protons are harnessed to export materials from the cell, such as to export excess sodium and calcium ions from
the cytoplasm into the periplasm (from where they can exit freely across the porins). Such
exporters are called: the
calcium-proton antiporter and the sodium-proton antiporter.

Antiporters are transport proteins in which the two particles exchanged travel in opposite directions. Both symporters and
antiporters are examples of
facilitated diffusion - although transport through the transporter is by passive diffusion, which
the transporter protein assists or facilitates, it is indirectly driven by
active transport. Active transport requires the cell to
expend its own energy. In this case the active transporter is the ETC which uses the energy in the electrons derived by
oxidising fuels like glucose.

Energy can be neither created nor destroyed and what we are seeing is energy transform from one form to another, a
process called transduction. The energy that transports the protons in and out of the cell, the lactose and proline into the cell,
is ultimately derived from the chemical energy stored in the glucose fuel. When a fuel is oxidised, be it glucose or petrol in a
car engine, a tiny fraction of its mass is converted into mass, according to Einstein's equation E = mc^2, so ultimately the
energy that derives the cell comes from a fraction of the fuel mass.

The proton gradient is used to power other systems, apart from transporters. Protons funnelled through the
flagellar motor
power rotation of the
flagellum in swimming bacteria. It takes 1024 protons to bring about one revolution of the motor in
Escherichia coli. [Note that since the flagellar motor uses charged protons it is an electric motor, but one which uses positive
charge rather than electrons.] Clearly locomotion is energy expensive and bacteria only swim when the cost is outweighed by
the benefits. Many species alternate between non-motile cells feeding, growing and reproducing whilst attached to some
suitable surface or food material (the substrate) and swarmer cells who swim around in the water column (and which can also
feed, grow and reproduce, though their chief function is to locate a new food source to settle onto).

ATP synthetase (ATP synthase or ATPase) is an enzyme that is also powered by inflowing protons. ATPase consists of a
stalk, the F0 portion, and a more-or-less spherical bulb, the F1 part, which sits in the cytoplasm. Protons flow through a
channel in the F0 stalk into the F1 portion which contains the enzyme's active site. The role of this enzyme is to manufacture
adenosine trisphosphate (ATP) from adenosine diphosphate (ADP) and (inorganic) phosphate. ATP is a universal energy
currency - used by most cells to power most of their systems. It contains energy that ultimately came from the glucose fuel (or
whatever fuel was used) and the formation of ATP results in some energy being converted back into mass. It is rather like the
'tokens' that one might insert into an electricity meter, except that in this case the tokens actually contain the energy as well.
As the protons flow through the ATPase the F1 portion rotates, much in the same way that the flagella rotate, by converting
some of the energy of the flowing protons into rotatory kinetic energy. It is thought that this rotation is essential for the working
of the enzyme - that is that the rotational energy is converted into chemical energy stored in the ATP molecules. ATP made by
ATPase is the main source of energy for the cell, but it is not the only source - the proton gradient is used by many
transporters and by flagella directly - these systems do not require ATP for their operation (though ATP is required for their
synthesis and maintenance).

The Role of Oxygen

Electrons flowing into the ETS have to go somewhere if the flow of electrons is to continue. In aerobic respiration, every pair of
electrons recombines with a pair of protons in a reaction with oxygen, to form water, H2O. Oxygen is the
terminal electron
in the ETS. Since addition of electrons (and also addition of hydrogen) is reduction, the oxygen is reduced. Oxygen
is a strong oxidising agent, meaning that it is easily reduced (since reduction and oxidation are 'opposite' reactions and
generally occur together as one chemical is oxidised and another reduced in a
redox reaction or oxidoreduction reaction.
This means that a lot of energy is released when oxygen, a strong oxidiser, reacts with hydrogen, a strong reducer. Indeed, as
demonstrated in school labs, the reaction is explosive under normal conditions! [Of course the cell controls the process so
that it is not explosive!] The energy released is the ultimate source of the driving force which causes electrons to flow through
the ETS from the hydrogen carriers to oxygen. Remember OIL RIG: oxidation is loss of electrons, reduction is gain.


The process we have described so far is similar to that which occurs in mitochondria in most eukaryotic cells. Mitochondria
have two membranes, an outer membrane containing porins and an inner membrane with variously-shaped infoldings or
tubular projections called cristae (sing. crista). The cristae increase the surface area for packing in many electron transport
systems and ATPase molecules - the mitochondria is specialised for electron transport and uses oxygen to drive the ETS and
uses the resultant proton gradient to make ATP for the whole eukaryotic cell. Mitochondria have tiny genomes, having lost
many of their original functions and are now totally dependent on their host for survival and can not live in isolation. Likewise
the host is dependent on mitochondria. The host cell can not make ATP by electron transport in aerobic respiration without
mitochondria, but it does carry out glycolysis in the cytosol and then transports the end product, pyruvate, into the
mitochondria where it is used in Kreb's cycle which takes place in the mitochondrial matrix (the 'mitochondrial cytosol').
Mitochondria, however, are not capable of glycolysis. Free-living aerobic bacteria, in contrast, have to carry out glycolysis,
Kreb's cycle and electron transport all by themselves.
electron and proton transport in the bacterial cell envelope
In a number of protozoa that lack mitochondria, it would appear that they lost their mitochondria as a secondary adaptation to
living without oxygen, or with very little oxygen. Relics of mitochondria appear to remain as
mitosomes. The function of
mitosomes is not yet clearly ellucidated, but they appear to be involved in synthesising iron-sulphur clusters, which are
required for some proteins, including many proteins involved in electron transport. Thus, they retain one of the functions of
mitochondria, but unlike mitochondria they have no genome of their own, instead relics of the mitochondrial genome seem to
be incorporated into the main nuclear genome of the cell. Mitosomes seem to represent a final stage in the evolutionary
sequence from endosymbiont to organelle.

Respiration Without Oxygen

Bacteria existed on the ancient Earth long before the earth had an oxygen-rich atmosphere. Many bacteria are still aerobic,
either facultatively, using oxygen when available in aerobic respiration, undergoing anaerobic respiration otherwise. To others
even trace amounts of oxygen are lethal!

Fermentation is a form of anaerobic respiration which does not use oxygen and the electron transport chain or the ATPase
F0/F1 complex. Instead the final oxidised product is another organic molecule. Glycolysis is one such fermentation, in which
glucose is fermented to pyruvate by incomplete oxidation. Since the oxidation of the fuel is incomplete not all of the available
chemical energy is extracted. glycolysis does not provide as much energy as aerobic respiration, indeed in aerobic
respiration, pyruvate produced by glycoslysis is further oxidised by the Kreb's cycle and by the ETS, involving oxygen as the
final oxidant or terminal electron acceptor. However, glycolysis does produce some ATP by a different process. Typically, the
pyruvate is further metabolised, sometimes yielding more ATP and/or other essential products, but the final product is still an
organic molecule and oxidation is incomplete. In aerobic respiration oxidation is complete and the end products are water and
carbon dioxide. There are many final fermentation products, depending on the species and its fermentation chemical pathway.
These final products are often excreted as waste products. For example,
Lactobacilli produce lactic acid, Propionibacteria,
propionic acid.

Fermentation also occurs in eukaryotes. In yeast, anaerobic respiration consists of glycolysis and then a series of reactions
that process the pyruvate into ethanol (alcohol). In animal muscle cells respiring anaerobically during short bursts of very
intense exercise, such as when sprinting, glycolysis produces pyruvate and this is then converted into lactic acid.

Other bacteria can do more than ferment their fuel in the absence of oxygen, they can undergo complete
, oxidising the fuel completely by using the ETS but without oxygen. Instead some other good oxidant acts as the
final electron-acceptor. For example, sulphur, sulphate, sulphite and thiosulphate may be used by sulphur-oxidising bacteria.
Iron slats may be used, in which iron ions are reduced to elemental iron; this occurs in many bacteria living on the surface of
rocks, such as in deserts, in which electrons from the ETS travel down pili, acting as nanowires, to the iron-salt containing
rocks on which the bacteria grow, so that the final electron acceptor is actually outside the cell. Other bacteria use nitrate,
nitrite, fumarate (an organic molecule which is produced from pyruvate in fermentation by some bacteria)  or carbon dioxide.
These are not as strongly oxidising as oxygen, so the energy yield may not be as high, but they are nearly as good and in
some habitats their use makes sense. For example, in many sediments oxygen may be lacking and sulphur may be abundant,
in which case using sulphur is clearly advantageous.

Autotrophs and Heterotrophs

Bacteria like Escherichia coli can metabolise a variety of fuels, but all these fuels are carbon-based organic molecules, such
as sugars, amino acids and some bacteria can utilise organic acids (purple bacteria) and lipids (fats and oils) such as
Staphylococcus which can feed on human skin oils. Some bacteria can also utilise hydrocarbons as fuel. In all these cases the
organism uses the fuel as both an energy source and a carbon source. Carbon is an essential nutrient as it forms the
backbone of organic molecules that make up the cell, such as proteins, nucleic acids, carbohydrates and lipids. These
bacteria are called
chemoheterotrophs. 'Chemo' refers to their use of chemicals as an energy source (fuel), whilst 'hetero'
refers to their use of organic molecules as carbon sources. These fuels / carbon-sources are organic and so they have been
synthesised by other organisms. Such bacteria feed on the decomposing remains of other organisms, or else parasitise them
as pathogens.
Chemotrophs use chemical reactions as their primary energy source; heterotrophs use pre-made organic
molecules as a carbon source.

Autotrophs, however, obtain their carbon from inorganic sources, which may be produced by other living things or may be
produced by simple geological processes. Such sources include carbon dioxide gas and methane.
Chemoautotrophs still
use chemicals as an energy source, but utilise inorganic carbon sources. The reason for this arrangement is that such
organisms frequently use inorganic chemicals as an energy source, so they can survive without pre-made organic molecules.
Chemoautotrophy is unique to bacteria though some organisms harvest these bacteria as symbionts to supply their own
needs (such as certain
pogonophoran worms in volcanic vents). Chemoautotrophy typically supplies energy at a relatively low
rate and so these organisms are often slow growing. Most can survive entirely on inorganic materials (rocks), water, carbon
dioxide and oxygen. Many are referred to as
chemolithotrophs - rock-eating organisms. It is remarkable to think that life can
grow on such minimal resources! Indeed, some chemoautotrophs thrive far beneath the surface of the earth, deep inside rock
deposits, 2 to 3 miles, perhaps more, beneath the Earth's surface. It is thought that it takes as long as 100 years for some of
these organisms to reproduce!

In all cases energy is harnessed by redox reactions - oxidising an organic fuel or an inorganic fuel. Some chemoautotrophs
harness energy by oxidising hydrogen to water. Anyone who has ever put a lighted splint to a test-tube of hydrogen will know
that this reaction releases large amounts of energy!
Thiobacillus ferooxidans is the best-studied example of an organism that
uses iron salts, oxidising iron(II) sulphate to iron(III) sulphate using sulphuric acid generated as a waste product by
sulphur-oxidising organisms. The latter can excrete enough sulphuric acid to carve out entire subterranean caves in
acid-soluble rocks such as limestone! Some species of
Thiobacillus are sulphur-oxidisers can also oxidise sulphur to sulphuric
acid, hydrogen sulphide to sulphuric acid and thiosulphate to sulphate.
Nitrifying bacteria (see nitrogen cycle) can oxidise
ammonium to nitrite or nitrite to nitrate.

Some chemoautotrophs can oxidise single-carbon molecules, e.g. methane, formaldehyde (methanal, HCHO) or methanol.
methane, for example, is found in coal and oil deposits and is oxidised to methanol. Methanol, produced by decomposition, is
oxidised to methanal, which is oxidised to methanoic acid, which is oxidised to carbon dioxide.

Using Light

Phototrophs are organisms that power themselves primarily using light energy rather than chemical reactions. Plants are
photoautotrophs - they use light as an energy source and carbon dioxide as a carbon-source. Of course plant cells contain
mitochondria that can respire fuels like glucose, in a chemoheterotrophic manner, but the glucose was first manufactured by
the plant photoautotrophically in photosynthesise, so light remains the primary energy source. Many bacteria are also
phototrophic. The
cyanobacteria are photoautotrophs, using inorganic carbon to build organic molecules in photosynthesis.
Purple bacteria can grow photoautotrophically or photoheterotrophically.

Photoheterotrophs use light as an energy source but obtain their carbon from pre-made organic sources. Another example
are the
halobacteria (a type of archaeobacteria).

All in all, bacteria (or prokaryotes if you do not consider archaebacteria to be 'bacteria') can produce energy and obtain
carbon in more different ways than any other group of organisms on Earth. This probably reflects their ancient lineage,
colonising the earth when it was very different than it is today with some groups adapting to the new biosphere, others
persisting in strange and harsh environments, such as deep beneath the Earth's surface, in anoxic sediments and in volcanic
According to the endosymbiotic theory mitochondria evolved
from free-living prokaryotes that became internalised inside
early cells. As the two co-evolved they became critically
dependant on one-another. Earlier stages in this process can
still be seen in the protozoan
Mixotricha paradoxa which lacks
mitochondria and so engulfs bacteria which it uses as a source
of ATP. One organism living inside another, especially within its
cells, is called an endosymbiont. Endosymbiosis is a common
phenomenon and mitochondria have many features
characteristic of prokaryotes, including there own genome, a
small circular double-strand of DNA. See
respiration for more
about mitochondria.
A mitochondrion in section.
A molecular model of ATPase produced (if I remember correctly!) using the
SWISS-MODEL online service - send a DNA sequence, which can be taken
from an online library, and they will send you the model which can be viewed
in their own software or plotted in Pov-Ray.