In order to function,
every machine requires specific parts such as the screws, springs, cams,
gears, and pulleys. Likewise, all biological machines must have many
well-engineered parts to work. Examples include units called organs
such as the liver, kidney, and heart. These complex life units are made
from still smaller parts called cells which in turn are constructed
from yet smaller machines known as organelles. Cell organelles
include mitochondria, Golgi complexes, microtubules, and centrioles.
Even below this level are other parts so small that they are formally
classified as macromolecules (large molecules).
A critically important
macromoleculearguably second in importance only to DNAis
ATP. ATP is a complex nanomachine that serves as the primary
energy currency of the cell (Trefil, 1992, p.93). A nanomachine is a
complex precision microscopic-sized machine that fits the standard definition
of a machine. ATP is the most widely distributed high-energy compound
within the human body (Ritter, 1996, p. 301). This ubiquitous
molecule is used to build complex molecules, contract muscles,
generate electricity in nerves, and light fireflies. All fuel sources
of Nature, all foodstuffs of living things, produce ATP, which in turn
powers virtually every activity of the cell and organism. Imagine the
metabolic confusion if this were not so: Each of the diverse foodstuffs
would generate different energy currencies and each of the great variety
of cellular functions would have to trade in its unique currency
(Kornberg, 1989, p. 62).
ATP is an abbreviation
for adenosine triphosphate, a complex molecule that contains
the nucleoside adenosine and a tail consisting of three phosphates.
(See Figure 1 for a simple structural formula and a space filled model
of ATP.) As far as known, all organisms from the simplest bacteria to
humans use ATP as their primary energy currency. The energy level it
carries is just the right amount for most biological reactions. Nutrients
contain energy in low-energy covalent bonds which are not very useful
to do most of kinds of work in the cells.
Figure 1. Views of ATP and related structures.
These low energy bonds
must be translated to high energy bonds, and this is a role of ATP.
A steady supply of ATP is so critical that a poison which attacks any
of the proteins used in ATP production kills the organism in minutes.
Certain cyanide compounds, for example, are poisonous because they bind
to the copper atom in cytochrome oxidase. This binding blocks the electron
transport system in the mitochondria where ATP manufacture occurs (Goodsell,
Energy is usually liberated
from the ATP molecule to do work in the cell by a reaction that removes
one of the phosphate-oxygen groups, leaving adenosine diphosphate
(ADP). When the ATP converts to ADP, the ATP is said to be spent.
Then the ADP is usually immediately recycled in the mitochondria where
it is recharged and comes out again as ATP. In the words of Trefil (1992,
p. 93) hooking and unhooking that last phosphate [on ATP] is what
keeps the whole world operating.
The enormous amount of
activity that occurs inside each of the approximately one hundred trillion
human cells is shown by the fact that at any instant each cell contains
about one billion ATP molecules. This amount is sufficient for
that cells needs for only a few minutes and must be rapidly recycled.
Given a hundred trillion cells in the average male, about 1023
or one sextillion ATP molecules normally exist in the body. For each
ATP the terminal phosphate is added and removed 3 times each minute
(Kornberg, 1989, p. 65).
The total human body content
of ATP is only about 50 grams, which must be constantly recycled every
day. The ultimate source of energy for constructing ATP is food; ATP
is simply the carrier and regulation-storage unit of energy. The average
daily intake of 2,500 food calories translates into a turnover of a
whopping 180 kg (400 lbs) of ATP (Kornberg, 1989, p. 65).
ATP contains the purine
base adenine and the sugar ribose which together form
the nucleoside adenosine. The basic building blocks used to construct
ATP are carbon, hydrogen, nitrogen, oxygen, and phosphorus which are
assembled in a complex that contains the number of subatomic parts equivalent
to over 500 hydrogen atoms. One phosphate ester bond and two phosphate
anhydride bonds hold the three phosphates (PO4)
and the ribose together. The construction also contains a b-N glycoside
bond holding the ribose and the adenine together.
Phosphates are well-known
high-energy molecules, meaning that comparatively high levels of energy
are released when the phosphate groups are removed. Actually, the high
energy content is not the result of simply the phosphate bond but the
total interaction of all the atoms within the ATP molecule.
Because the amount of
energy released when the phosphate bond is broken is very close to that
needed by the typical biological reaction, little energy is wasted.
Generally, ATP is connected to another reactiona process called
coupling which means the two reactions occur at the same time
and at the same place, usually utilizing the same enzyme complex. Release
of phosphate from ATP is exothermic (a reaction that gives off heat)
and the reaction it is connected to is endothermic (requires energy
input in order to occur). The terminal phosphate group is then transferred
by hydrolysis to another compound, a process called phosphorylation,
producing ADP, phosphate (Pi)
Figure 2. The two-dimensional stick model
of adenosine phosphate family of molecules, showing the atom and bond
The self-regulation system
of ATP has been described as follows:
The high-energy bonds
of ATP are actually rather unstable bonds. Because they are unstable,
the energy of ATP is readily released when ATP is hydrolyzed in cellular
reactions. Note that ATP is an energy-coupling agent and not
a fuel. It is not a storehouse of energy set aside for some future need.
Rather it is produced by one set of reactions and is almost immediately
consumed by another. ATP is formed as it is needed, primarily by oxidative
processes in the mitochondria. Oxygen is not consumed unless ADP and
a phosphate molecule are available, and these do not become available
until ATP is hydrolyzed by some energy-consuming process. Energy
metabolism is therefore mostly self-regulating (Hickman, Roberts,
and Larson, 1997, p.43). [Italics mine]
ATP is not excessively
unstable, but it is designed so that its hydrolysis is slow in the absence
of a catalyst. This insures that its stored energy is released
only in the presence of the appropriate enzyme (McMurry and Castellion,
1996, p. 601).
The ATP is used for many
cell functions including transport work moving substances across
cell membranes. It is also used for mechanical work, supplying
the energy needed for muscle contraction. It supplies energy not only
to heart muscle (for blood circulation) and skeletal muscle (such as
for gross body movement), but also to the chromosomes and flagella to
enable them to carry out their many functions. A major role of ATP is
in chemical work, supplying the needed energy to synthesize the
multi-thousands of types of macromolecules that the cell needs to exist.
ATP is also used as an
on-off switch both to control chemical reactions and to send messages.
The shape of the protein chains that produce the building blocks and
other structures used in life is mostly determined by weak chemical
bonds that are easily broken and remade. These chains can shorten, lengthen,
and change shape in response to the input or withdrawal of energy. The
changes in the chains alter the shape of the protein and can also alter
its function or cause it to become either active or inactive.
The ATP molecule
can bond to one part of a protein molecule, causing another part of
the same molecule to slide or move slightly which causes it to change
its conformation, inactivating the molecule. Subsequent removal of ATP
causes the protein to return to its original shape, and thus it is again
functional. The cycle can be repeated until the molecule is recycled,
effectively serving as an on and off switch (Hoagland and Dodson, 1995,
p.104). Both adding a phosphorus (phosphorylation) and removing a phosphorus
from a protein (dephosphorylation) can serve as either an on or an off
How is ATP
ATP is manufactured as
a result of several cell processes including fermentation, respiration
and photosynthesis. Most commonly the cells use ADP as a precursor molecule
and then add a phosphorus to it. In eukaryotes this can occur either
in the soluble portion of the cytoplasm (cytosol) or in special energy-producing
structures called mitochondria. Charging ADP to form ATP in the mitochondria
is called chemiosmotic phosphorylation. This process occurs in
specially constructed chambers located in the mitochondrions inner
Figure 3. An Outline
of the ATP-synthase macro-molecule showing its subunits and nanomachine
traits. ATP-synthase converts ADP into ATP, a process called charging.
Shown behind ATP-synthase is the membrane in which the ATP-synthase
is mounted. For the ATP that is charged in the mitochondria, ATP-synthase
is located in the inner membrane.
The mitochondrion itself
functions to produce an electrical chemical gradientsomewhat like
a batteryby accumulating hydrogen ions in the space between the
inner and outer membrane. This energy comes from the estimated 10,000
enzyme chains in the membranous sacks on the mitochondrial walls. Most
of the food energy for most organisms is produced by the electron transport
chain. Cellular oxidation in the Krebs cycle causes an electron build-up
that is used to push H+
ions outward across the inner mitochondrial membrane (Hickman et al.,
1997, p. 71).
As the charge builds up,
it provides an electrical potential that releases its energy by causing
a flow of hydrogen ions across the inner membrane into the inner chamber.
The energy causes an enzyme to be attached to ADP which catalyzes the
addition of a third phosphorus to form ATP. Plants can also produce
ATP in this manner in their mitochondria but plants can also produce
ATP by using the energy of sunlight in chloroplasts as discussed later.
In the case of eukaryotic animals the energy comes from food which is
converted to pyruvate and then to acetyl coenzyme A (acetyl CoA).
Acetyl CoA then enters the Krebs cycle which releases energy that results
in the conversion of ADP back into ATP.
How does this potential
difference serve to reattach the phosphates on ADP molecules? The more
protons there are in an area, the more they repel each other. When the
repulsion reaches a certain level, the hydrogens ions are forced out
of a revolving-door-like structure mounted on the inner mitochondria
membrane called ATP synthase complexes. This enzyme functions
to reattach the phosphates to the ADP molecules, again forming ATP.
The ATP synthase revolving
door resembles a molecular water wheel that harnesses the flow of hydrogen
ions in order to build ATP molecules. Each revolution of the wheel requires
the energy of about nine hydrogen ions returning into the mitochondrial
inner chamber (Goodsell, 1996, p.74). Located on the ATP synthase are
three active sites, each of which converts ADP to ATP with every turn
of the wheel. Under maximum conditions, the ATP synthase wheel turns
at a rate of up to 200 revolutions per second, producing 600 ATPs during
ATP is used in conjunction
with enzymes to cause certain molecules to bond together. The correct
molecule first docks in the active site of the enzyme along with an
ATP molecule. The enzyme then catalyzes the transfer of one of the ATP
phosphates to the molecule, thereby transferring the energy stored in
the ATP molecule. Next a second molecule docks nearby at a second
active site on the enzyme. The phosphate is then transferred to it,
providing the energy needed to bond the two molecules now attached to
the enzyme. Once they are bonded, the new molecule is released. This
operation is similar to using a mechanical jig to properly position
two pieces of metal which are then welded together. Once welded, they
are released as a unit and the process then can begin again.
Although ATP contains
the amount of energy necessary for most reactions, at times more energy
is required. The solution is for ATP to release two phosphates
instead of one, producing an adenosine monophosphate (AMP) plus a chain
of two phosphates called a pyrophosphate. How adenosine monophosphate
is built up into ATP again illustrates the precision and the complexity
of the cell energy system. The enzymes used in glycolysis, the citric
acid cycle, and the electron transport system, are all so precise that
they will replace only a single phosphate. They cannot add two
new phosphates to an AMP molecule to form ATP.
The solution is an intricate
enzyme called adenylate kinase which transfers a single
phosphate from an ATP to the AMP, producing two ADP molecules.
The two ADP molecules can then enter the normal Krebs cycle designed
to convert ADP into ATP. Adenylate kinase requires an atom of magnesiumand
this is one of the reasons why sufficient dietary magnesium is important.
Adenylate kinase is a
highly organized but compact enzyme with its active site located deep
within the molecule. The deep active site is required because the reactions
it catalyzes are sensitive to water. If water molecules lodged between
the ATP and the AMP, then the phosphate might break ATP into ADP and
a free phosphate instead of transferring a phosphate from ATP to AMP
to form ADP.
To prevent this, adenylate
kinase is designed so that the active site is at the end of a
channel deep in the structure which closes around AMP and ATP, shielding
the reaction from water. Many other enzymes that use ATP rely on this
system to shelter their active site to prevent inappropriate reactions
from occurring. This system ensures that the only waste that occurs
is the normal wear, tear, repair, and replacement of the cells
Pyrophosphates and pyrophosphoric
acid, both inorganic forms of phosphorus, must also be broken down so
they can be recycled. This phosphate breakdown is accomplished by the
inorganic enzyme pyrophosphatase which splits the pyrophosphate
to form two free phosphates that can be used to charge ATP (Goodsell,
1996, p.79). This system is so amazingly efficient that it produces
virtually no waste, which is astounding considering its enormously detailed
structure. Goodsell (1996, p. 79) adds that our energy-producing
machinery is designed for the production of ATP; quickly, efficiently,
and in large quantity.
The main energy carrier
the body uses is ATP, but other energized nucleotides are also utilized
such as thymine, guanine, uracil, and cytosine for making RNA and DNA.
The Krebs cycle charges only ADP, but the energy contained in ATP can
be transferred to one of the other nucleosides by means of an enzyme
called nucleoside diphosphate kinase. This enzyme transfers the
phosphate from a nucleoside triphosphate, commonly ATP, to a nucleoside
diphosphate such as guanosine diphosphate (GDP) to form guanosine triphosphate
The nucleoside diphosphate
kinase works by one of its six active sites binding nucleoside triphosphate
and releasing the phosphate which is bonded to a histidine. Then the
nucleoside triphosphate, which is now a diphosphate, is released, and
a different nucleoside diphosphate binds to the same siteand as
a result the phosphate that is bonded to the enzyme is transferred,
forming a new triphosphate. Scores of other enzymes exist in order for
ATP to transfer its energy to the various places where it is needed.
Each enzyme must be specifically designed to carry out its unique function,
and most of these enzymes are critical for health and life.
The body does contain
some flexibility, and sometimes life is possible when one of these enzymes
is defectivebut the person is often handicapped. Also, back-up
mechanisms sometimes exist so that the body can achieve the same goals
through an alternative biochemical route. These few simple examples
eloquently illustrate the concept of over-design built into the body.
They also prove the enormous complexity of the body and its biochemistry.
The Message of the Molecule
Without ATP, life as we
understand it could not exist. It is a perfectly-designed, intricate
molecule that serves a critical role in providing the proper size energy
packet for scores of thousands of classes of reactions that occur in
all forms of life. Even viruses rely on an ATP molecule identical to
that used in humans. The ATP energy system is quick, highly efficient,
produces a rapid turnover of ATP, and can rapidly respond to energy
demand changes (Goodsell, 1996, p.79).
Furthermore, the ATP molecule
is so enormously intricate that we are just now beginning to understand
how it works. Each ATP molecule is over 500 atomic mass units (500 u).
In manufacturing terms, the ATP molecule is a machine with a level of
organization on the order of a research microscope or a standard television
(Darnell, Lodish, and Baltimore, 1996).
Among the questions evolutionists
must answer include the following, How did life exist before ATP?
How could life survive without ATP since no form of life we know
of today can do that? and How could ATP evolve and where
are the many transitional forms required to evolve the complex ATP molecule?
No feasible candidates exist and none can exist because only a perfect
ATP molecule can properly carry out its role in the cell.
In addition, a potential
ATP candidate molecule would not be selected for by evolution until
it was functional and life could not exist without ATP or a similar
molecule that would have the same function. ATP is an example of a molecule
that displays irreducible complexity which cannot be simplified
and still function (Behe, 1996). ATP could have been created only as
a unit to function immediately in life and the same is true of the other
intricate energy molecules used in life such as GTP.
Although other energy
molecules can be used for certain cell functions, none can even come
close to satisfactorily replacing all the many functions of ATP. Over
100,000 other detailed molecules like ATP have also been designed to
enable humans to live, and all the same problems related to their origin
exist for them all. Many macromolecules that have greater detail than
ATP exist, as do a few that are less highly organized, and in order
for life to exist all of them must work together as a unit.
between Prokaryotic and
An enormous gap exists
between prokaryote (bacteria and cyanobacteria) cells and eukaryote
(protists, plants and animals) type of cells:
...prokaryotes and eukaryotes
are profoundly different from each other and clearly represent a marked
dichotomy in the evolution of life. . . The organizational complexity
of the eukaryotes is so much greater than that of the prokaryotes that
it is difficult to visualize how a eukaryote could have arisen from
any known prokaryote (Hickman et al., 1997, p. 39).
Some of the differences
are that prokaryotes lack organelles, a cytoskeleton, and most of the
other structures present in eukaryotic cells. Consequently, the functions
of most organelles and other ultrastructure cell parts must be performed
in bacteria by the cell membrane and its infoldings called mesosomes.
Major Methods of Producing ATP
A crucial difference between
prokaryotes and eukaryotes is the means they use to produce ATP. All
life produces ATP by three basic chemical methods only: oxidative phosphorylation,
photophosphorylation, and substrate-level phosphorylation (Lim, 1998,
p. 149). In prokaryotes ATP is produced both in the cell wall and in
the cytosol by glycolysis. In eukaryotes most ATP is produced in chloroplasts
(for plants), or in mitochondria (for both plants and animals). No means
of producing ATP exists that is intermediate between these four basic
methods and no transitional forms have ever been found that bridge the
gap between these four different forms of ATP production. The machinery
required to manufacture ATP is so intricate that viruses are not able
to make their own ATP. They require cells to manufacture it and viruses
have no source of energy apart from cells.
In prokaryotes the cell
membrane takes care of not only the cells energy-conversion needs,
but also nutrient processing, synthesizing of structural macromolecules,
and secretion of the many enzymes needed for life (Talaro and Talaro,
1993, p. 77). The cell membrane must, for this reason be compared with
the entire eukaryote cell ultrastructure which performs these
many functions. No simple means of producing ATP is known and prokaryotes
are not by any means simple. They contain over 5,000 different kinds
of molecules and can use sunlight, organic compounds such as carbohydrates
and inorganic compounds as sources of energy to manufacture ATP.
Another example of the
cell membrane in prokaryotes assuming a function of the eukaryotic cell
ultrastructure is as follows: Their DNA is physically attached to the
bacterial cell membrane and DNA replication may be initiated by changes
in the membrane. These membrane changes are in turn related to the bacteriums
growth. Further, the mesosome appears to guide the duplicated chromatin
bodies into the two daughter cells during cell division (Talaro and
In eukaryotes the mitochondria
produce most of the cells ATP (anaerobic glycolysis also produces
some) and in plants the chloroplasts can also service this function.
The mitochondria produce ATP in their internal membrane system called
the cristae. Since bacteria lack mitochondria, as well as an internal
membrane system, they must produce ATP in their cell membrane which
they do by two basic steps. The bacterial cell membrane contains a unique
structure designed to produce ATP and no comparable structure has been
found in any eukaryotic cell (Jensen, Wright, and Robinson, 1997).
In bacteria, the ATPase
and the electron transport chain are located inside the cytoplasmic
membrane between the hydrophobic tails of the phospholipid membrane
inner and outer walls. Breakdown of sugar and other food causes the
positively charged protons on the outside of the membrane to
accumulate to a much higher concentration than they are on the membrane
inside. This creates an excess positive charge on the outside
of the membrane and a relatively negative charge on the inside.
The result of this charge
difference is a dissociation of H2O
molecules into H+
ions. The H+
ions that are produced are then transported outside of the cell and
ions remain on the inside. This results in a potential energy gradient
similar to that produced by charging a flashlight battery. The force
the potential energy gradient produces is called a proton motive
force that can accomplish a variety of cell tasks including converting
ADP into ATP.
In some bacteria such
as Halobacterium this system is modified by use of bacteriorhodopsin,
a protein similar to the sensory pigment rhodopsin used in the vertebrate
retina (Lim, 1998, p. 166). Illumination causes the pigment to absorb
light energy, temporarily changing rhodopsin from a trans to
a cis form. The trans to cis conversion causes deprotonation
and the transfer of protons across the plasma membrane to the periplasm.
The proton gradient that
results is used to drive ATP synthesis by use of the ATPase complex.
This modification allows bacteria to live in low oxygen but rich light
regions. This anaerobic ATP manufacturing system, which is unique to
prokaryotes, uses a chemical compound other than oxygen as a terminal
electron acceptor (Lim, 1998, p. 168). The location of the ATP producing
system is only one of many major contrasts that exist between bacterial
cell membranes and mitochondria.
Chloroplasts are double
membraned ATP-producing organelles found only in plants. Inside their
outer membrane is a set of thin membranes organized into flattened sacs
stacked up like coins called thylakoids (Greek thylac
or sack, and oid meaning like). The disks contain chlorophyll
pigments that absorb solar energy which is the ultimate source of energy
for all the plants needs including manufacturing carbohydrates
from carbon dioxide and water (Mader, 1996, p. 75). The chloroplasts
first convert the solar energy into ATP stored energy, which is then
used to manufacture storage carbohydrates which can be converted back
into ATP when energy is needed.
also possess an electron transport system for producing ATP. The electrons
that enter the system are taken from water. During photosynthesis, carbon
dioxide is reduced to a carbohydrate by energy obtained from ATP (Mader,
1996, p. 12). Photosynthesizing bacteria (cyanobacteria) use yet another
system. Cyanobacteria do not manufacture chloroplasts but use chlorophyll
bound to cytoplasmic thylakoids. Once again plausible transitional forms
have never been found that can link these two forms of ATP production
from the photosynthesis system.
The two most common evolutionary
theories of the origin of the mitochondria-chloroplast ATP production
system are 1) endosymbiosis of mitochondria and chloroplasts from the
bacterial membrane system and 2) the gradual evolution of the prokaryote
cell membrane system of ATP production into the mitochondria and chloroplast
systems. Believers in endosymbiosis teach that mitochondria were once
free-living bacteria, and that early in evolution ancestral eukaryotic
cells simply ate their future partners (Vogel, 1998, p. 1633).
Both the gradual conversion and endosymbiosis theory require many transitional
forms, each new one which must provide the animal with a competitive
advantage compared with the unaltered animals.
The many contrasts between
the prokaryotic and eukaryotic means of producing ATP, some of which
were noted above, are strong evidence against the endosymbiosis theory.
No intermediates to bridge these two systems has ever been found and
arguments put forth in the theorys support are all highly speculative.
These and other problems have recently become more evident as a result
of recent major challenges to the standard endosymbiosis theory. The
standard theory has recently been under attack from several fronts,
and some researchers are now arguing for a new theory:
Scientists pondering how
the first complex cell came together say the new idea could solve some
nagging problems with the prevailing theory... [the new theory
is]... elegantly argued, says Michael Gray of Dalhouisie University
in Halifax, Nova Scotia, but there are an awful lot of things
the hypothesis doesnt account for. In the standard picture
of eukaryote evolution, the mitochondrion was a lucky accident. First,
the ancestral cellprobably an archaebacterium, recent genetic
analyses suggestacquired the ability to engulf and digest complex
molecules. It began preying on its microbial companions. At some point,
however, this predatory cell didnt fully digest its prey, and
an even more successful cell resulted when an intended meal took up
permanent residence and became the mitochondrion. For years, scientists
had thought they had examples of the direct descendants of those primitive
eukaryotes: certain protists that lack mitochondria. But recent analysis
of the genes in those organisms suggests that they, too, once carried
mitochondria but lost them later (Science, 12 September 1997,
p. 1604). These findings hint that eukaryotes might somehow have acquired
their mitochondria before they had evolved the ability to engulf and
digest other cells (Vogel, 1998, p. 1633).
In this brief review we
have examined only one cell macromolecule, ATP, and the intricate mechanisms
which produce it. We have also looked at the detailed supporting mechanism
which allows the ATP molecule to function. ATP is only one of hundreds
of thousands of essential molecules, each one that has a story. As each
of those stories is told, they will stand as a tribute to both the genius
and the enormously complex design of the natural world. All the books
in the largest library in the world may not be able to contain the information
needed to understand and construct the estimated 100,000 complex macromolecule
machines used in humans. Much progress has been made in understanding
the structure and function of organic macromolecules and some of the
simpler ones are now being manufactured by pharmaceutical firms.
Now that scientists understand
how some of these highly organized molecules function and why they are
required for life, their origin must be explained. We know only four
basic methods of producing ATP: in bacterial cell walls, in the cytoplasm
by photosynthesis, in chloroplasts, and in mitochondria. No transitional
forms exist to bridge these four methods by evolution. According to
the concept of irreducible complexity, these ATP producing machines
must have been manufactured as functioning units and they could not
have evolved by Darwinism mechanisms. Anything less than an entire ATP
molecule will not function and a manufacturing plant which is less then
complete cannot produce a functioning ATP. Some believe that the field
of biochemistry which has achieved this understanding has already falsified
the Darwinian world view (Behe, 1996).*
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Did the first complex cell eat hydrogen? Science 279: 1633-1634.