In order to function,
every machine requires specific parts such as 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).
|Fig. 1. Views of ATP and related structures.
A critically important
macromoleculearguably “second in importance only to
DNA”is 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.
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, 1996, p.74).
How ATP Transfers Energy
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
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 cell’s 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.
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).
The Structure of ATP
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
|Fig. 2. The two-dimensional stick model of the adenosine phosphate family of molecules, showing the atom and bond arrangement.
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) and energy.
system of ATP has been described as follows:
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).
Function of ATP
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.
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 switch.
is ATP Produced?
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 mitochondrion’s inner membranes.
|Fig. 3. An outline of the ATP-synthase macromolecule 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.
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
to that molecule 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.
Double Energy Packet
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.
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 cell’s organelles.
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 (GTP).
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.
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,
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 AMUs). 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,
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.
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.
Contrast between Prokaryotic and
An enormous gap
exists between prokaryote (bacteria and cyanobacteria) cells and
eukaryote (protists, plants and animals) type of cells:
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.
Four 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.
the cell membrane takes care of not only the cell’s 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.
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 bacterium’s growth. Further, the
mesosome appears to guide the duplicated chromatin bodies into
the two daughter cells during cell division (Talaro and Talaro,
the mitochondria produce most of the cell’s 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+ and OH ions. The H+ ions that are produced are then transported
outside of the cell and the OH 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.
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 plant’s 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
this form of ATP production to the chloroplast 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 theory’s
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:
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 doesn’t 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 didn’t 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,
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 than 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).
Jerry Bergman has seven degrees, including
in biology, psychology, and evaluation and research, from Wayne State
University, in Detroit, Bowling Green State University in Ohio, and Medical
College of Ohio in Toledo. He has taught at Bowling Green State University,
the University of Toledo, Medical College of Ohio and at other colleges and
universities. He currently teaches biology, microbiology, biochemistry, and
human anatomy at the college level and is a research associate involved in
research in the area of cancer genetics. He has published widely in both
popular and scientific journals. [RETURN TO TOP]
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