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Bacteria Share Light Spectrum with Leaves

Photosynthesis is one of the most important chemical processes for the existence and surviving of the entire biosphere… Every plant and some microscopic organisms are capable of using light from the Sun to produce and store energy. See below an animation:

It’s another crucial example of complex biological mechanism which defies any plausible explanation from the evolutionary community, and delights theist views!

Plant leaves convert light into chemical energy for use in cells. Their biochemistry specifically absorbs the blue and red areas of the visible light spectrum. Now researchers have discovered that light-harvesting bacteria living on the surfaces of leaves gather energy from the green part of the spectrum, meaning that they cooperate rather than compete with plants. How did this perfectly balanced energy-sharing system come about?

Knowing that light-harvesting microbes live in aquatic environments, the researchers tested the hypothesis that similar bacteria live on leaves. They were right. And the light that the microbes gather was “compatible with the plant’s photosynthesis,” resulting in “a significant ecological advantage to microbes inhabiting this environment.”1

In a study published online in Environmental Microbiology, the research team screened genetic material from the surfaces of different leaves harvested from an oasis near the Dead Sea. They found genetic codes for specific types of rhodopsins, which are molecules that capture light. Some enable sight in vertebrate eyes, but many of the rhodopsins found on leaf surfaces were part of light-gathering apparatuses used by bacteria as tiny energy generators called “light-driven proton pumps.”1

The researchers found that the bacteria absorb the most light at exactly the same point where plants absorb no light.

Not only does the sharing of ecosystem resources between these species—as between plants and animals—indicate design,4 but the ingenious machinery required to capture and convert light into useful cellular energy points to an Engineer of surpassing brilliance.5

This was emphasized by yet another observation. The researchers found that the bacteria use some of their rhodopsins as light sensors so they can most effectively use the energy available to them. “This suggests that microorganisms in the phyllosphere [leaf surfaces] are intensively engaged in light sensing, to accommodate the effects of fluctuations in light quality, intensity and UV radiation at the leaf surface,” according to the study authors.1

From: ICR

References

  1. Atamna-Ismaeel, N. et al. Microbial rhodopsins on leaf surfaces of terrestrial plants. Environmental Microbiology. Published online <http://www.imls.uzh.ch/research/vonmering/publ/21883799.pdf>before print September 1, 2011.
  2. Darwin, C. 1859. On the Origin of Species by Means of Natural Selection: or The Preservation of Favoured Races in the Struggle of Life. New York: D. Appleton and Company.
  3. Mackay, J. Leaves and Microbes Share the Light. Evidence News. Creation Research. Posted on evidenceweb.net November 16, 2011, accessed November 29, 2011.
  4. Demick, D. 2000. The Unselfish Green GeneActs & Facts. 29 (7).
  5. Swindell, R. 2002. Shining Light on the Evolution of PhotosynthesisJournal of Creation (formerly TJ). 17 (3): 74-84.
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Algae Protein Masters Quantum Mechanics

 

Once again, the nature precedes the humankind on mastering wonderful technologies! Researchers have demonstrated that certain proteins can manipulate light waves to their advantage. These kinds of observations are a conundrum for evolution, which can’t explain such advanced biological capabilities.

Quantum mechanics represents mankind’s current approximation of the behavior of matter on the atomic and subatomic level. Experiments have shown that light, as well as electrons, can travel along two wave-like paths at the same time and yet arrive at the same place. In quantum-speak, these paths are said to exist in “coherence.”

Scientists have measured the control of light in coherence by a protein that is involved in photosynthesis. Certain proteins with molecular “antennae” are structured to capture and transfer light energy. When combined with a host of nearby―as well as faraway―protein machines, they use this energy to build the chemicals on which all other living things depend.

But remarkably, one particular type of algae is able to perform this function in low lighting. Most other plants shut down photosynthesis for the night, while “cryptophytes” continue to harvest light. According to a paper published in Nature, researchers discovered that the light-harvesting proteins used by the algae are structured differently from those of other plants and that their particular configuration can pick up low-light energy and hold it in coherence. They called these plants “coherently wired.”1

In order for these algae to harvest light in low-light conditions, their method of photosynthesis must be much more efficient than that of other plants. The “coherent” wiring of this protein enables “quantum effects [to] facilitate the efficient light-harvesting by cryptophyte algae.”1 The ingenious configuration that allows this protein to manipulate light adds to the list of similar finds that have been controversial because of their stunningly skillful construction.

How could evolution by selective pressure ever achieve such marvels of engineering? Assuming that some evolutionary ancestor of cryptophytes performed normal “high light” photosynthesis like other plants, it is very speculative to assert that there ever could have been enough selective pressure and fortuitous mutations to have altered this plant’s machinery with such exacting precision—all just to enable it to live in a slightly different environmental niche.

Earlier, a 2006 study showed that quantum tunneling occurs in a protein system. In their study published in Science, the authors wrote, “The question of whether enzymes have evolved to use quantum tunneling to the best advantage has provoked a heated debate.”As well it should.

Truly, these tiny algae cells have been constructed with remarkable skill. A University of Toronto press release stated that their light-harvesting strategy “suggests that algae knew about quantum mechanics nearly two billion years before humans.”3

by Brian Thomas, M.S.

See more in: http://www.icr.org/article/algae-molecule-masters-quantum-mechanics/

 

References

  1. Collini, E. et al. 2010. Coherently wired light-harvesting in photosynthetic marine algae at ambient temperatureNature. 463 (7281): 644-647.
  2. Masgrau, L. et al. 2006. Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling.Science. 312 (5771): 237-241.
  3. Bettam, S. Scientists find quantum mechanics at work in photosynthesisNews @ the University of Toronto. Posted on news.utoronto.ca February 3, 2010, accessed February 4, 2010.

Our inverted retina: Not a bad design

Evolutionists frequently maintain that the vertebrate retina exhibits a feature which indicates that it was not designed because its organisation appears to be less than ideal. They refer to the fact that for light to reach the photoreceptors it has to pass through the bulk of the retina’s neural apparatus, and presume that consequent degradation of the image formed at the level of the photoreceptors occurs. In biological terms this arrangement of the retina is said to be inverted because the visual cells are oriented so that their sensory ends are directed away from incident light. It is typical of vertebrates but rare among invertebrates, being seen in a few molluscs and arachnids.

 

 

 

 

 

 

As usual, evolutionists like to point this out as an evidence of “bad design”, thus, being supposedly more explainable under the light of natural, unguided view. Dawkins, while admitting that light traversing the inverted retina is not disturbed significantly during its passage to the photoreceptors, writes as follows :

‘Any engineer would naturally assume that the photocells would point towards the light, with their wires leading backwards towards the brain. He would laugh at any suggestion that the photocells might point away, from the light, with their wires departing on the side nearest the light. Yet this is exactly what happens in all vertebrate retinas. Each photocell is, in effect, wired in backwards, with its wire sticking out on the side nearest the light. The wire has to travel over the surface of the retina to a point where it dives through a hole in the retina (the so-called ‘blind spot’) to join the optic nerve. This means that the light, instead of being granted an unrestricted passage to the photocells, has to pass through a forest of connecting wires, presumably suffering at least some attenuation and distortion (actually, probably not much but, still, it is the principle of the thing that would offend any tidy-minded engineer). I don’t know the exact explanation for this strange state of affairs. The relevant period of evolution is so long ago.’ 1

First, we must review some things about ocular anatomy:

 

Figure 2Light enters the human eye via the transparent cornea, the eye’s front window, which acts as a powerful convex lens. After passing through the pupil (the aperture in the iris diaphragm) light is further refracted by the crystalline lens. An image of the external environment is thus focused on the retina which transduces light into neural signals and is the innermost (relative to the geometric centre of the eyeball) of the three tunics of the eye’s posterior segment. The other two tunics of the eye’s posterior segment are the white tough fibrous sclera which is outermost and continuous with the cornea anteriorly, and thechoroid, a pigmented and highly vascular layer which lies sandwiched between the retina and sclera.

The retina consists of ten layers, of which the outermost is the dark retinal pigment epithelium (RPE) which because of its melanin pigment is opaque to light. The RPE cells have fine hair-like projections on their inner surface called microvilli which lie between and ensheath the tips of the photoreceptor outer segments. There is thus a potential plane of cleavage between the RPE and the photoreceptors which is manifested when the neurosensory retina becomes separated from the RPE, e.g. as a result of injury, a condition known as retinal detachment.

Each photoreceptor, whether rod or cone, consists of an inner and an outer segment, the former having organelles (intracellular apparatus) for manufacturing the visual pigment present in the latter. The rod and cone layer and all eight layers internal to it constitute (in distinction from the RPE) what is known as the neurosensory retina which is virtually transparent to light. By means of many complex nerve connections within the neurosensory retina, electrical impulses generated by light reaching the photoreceptors are processed and transmitted to the retina’s nerve fibre layer and thence pass up the optic nerve to the brain.

In many species for whom vision in very low levels of illumination is important, a layer of reflective crystalline material, the tapetum (Latin: carpet) is incorporated in the RPE or choroid.1 Acting as a mirror, the tapetum reflects light which has passed between the photoreceptors, so augmenting the light bombarding the photoreceptors. Hence the proverbial ‘cat’s eyes’ when caught by a beam of light in the dark.

The retinal pigment epithelium

Fundamental to understanding the inverted retina is the crucial role played by the RPE. Many of its important functions are now well known. Each RPE cell is in intimate contact with the tips of 20 or more photoreceptor outer segments which number over 130 million. Without the RPE the photoreceptors and the rest of the neurosensory retina cannot function normally and ultimately atrophy.

The outer segment of a photoreceptor consists of a stack of discs containing light-sensitive photopigment. These discs are being continually formed by the inner segment from where they move in succession outwards in the outer segment towards the RPE which phagocytoses (Greek: φάγω (phagō) = eat) them and recycles their chemical components.

The RPE stores vitamin A, a precursor of the photopigments, and thus participates in their regeneration. There are four photopigments which are all bleached on exposure to light: rhodopsin (found in the rods, for night vision) and one for each of the three different types of cones (one for each of the primary colours). It synthesises glycosaminoglycans for the interphotoreceptor matrix, i.e. the material lying between and separating the photoreceptors.

Besides oxygen, the RPE selectively transports nutrients from the choroid to supply the outer third of the retina and removes the waste products of photoreceptor metabolism to be cleared by the choroidal circulation. By selective pumping of metabolites and the presence of its tight intercellular junctions, the RPE acts as a barrier, called the blood-retinal barrier, preventing access of larger or harmful chemicals to retinal tissue, thereby contributing to the maintenance of a stable and optimal retinal environment.

The RPE has complex mechanisms for dealing with toxic molecules and free radicals produced by the action of light. Specific enzymes such as the superoxide dismutases, catalases, and peroxidases are present to catalyse the breakdown of potentially harmful molecules such as superoxide and hydrogen peroxide. Antioxidants such as a-tocopherol (vitamin E) and ascorbic acid (vitamin C) are available to reduce oxidative damage.

Our photoreceptors thus continually synthesise new outer segment discs with their specific photopigments, recycling materials from used discs digested by the RPE. This prompts the question, ‘Why have such a complicated process?’ The answer must be that it is an example of biological renewal, by means of which tissues exposed to damaging chemicals, radiation, mechanical trauma, etc., are able to survive. Without self renewal, tissues such as the skin, the lining of the gut, blood cells etc would quickly accumulate fatal defects. In the same way, by the continual replacing of their discs the photoreceptors counter the relentless process of disintegration accelerated by toxic agents, particularly short wavelength light.

 

The choroidal heat sink

 

It has been observed that the damage to photoreceptors in an experimental model is strongly related to temperature, and other studies have confirmed that heat exacerbates photochemical injury. Any system designed to protect against the latter should also protect against the former. In 1980, a paper was published which explained for the first time something already known about the choroid.2 That is, its very high rate of blood flow which far exceeds the nutritional needs of the retina, despite the latter being highly active metabolically, as indicated.

The choroidal capillaries (the choriocapillaris) form a rich plexus lying immediately external to the RPE, predominantly its central area, and separated from it by only a very thin membrane (Bruch’s). The absorption of excess light by the RPE produces heat in the outer retina which has to be dissipated if thermal damage to the delicate and complex biological machinery, its own and that of its neighbourhood, is to be avoided.

The authors of this study cogently argue that an important function of the choroid with its torrential blood flow (in local terms) and its close proximity to the RPE, is to act as a heat sink and cooling device. Still more fascinating are the results of further studies by the same workers indicating that there are central (via the brain), light-mediated nervous reflexes regulating choroidal blood flow, increasing the blood flow with increased illumination. Both RPE and choroid are essential for vision, but they are opaque, so it follows that for light to reach the photoreceptors, both RPE and choroid have to be located external to the neurosensory retina; hence we can conclude that there are sound reasons for the inverted configuration of the human and vertebrate retina.

 

The foveola

Although the neurosensory retina is virtually transparent apart from the blood in its very slender blood vessels, there is an additional refinement of its structure in its central region called the macula. The retina and the occipital cerebral cortex (called the visual cortex) of the brain, to which the former transmits visual information, are so organised that the VA is maximal in the visual axis. The visual axis passes through the foveola which forms the floor of a circular pit with a sloping wall, the fovea (Latin: pit) at the centre of the macula. Away from the fovea the VA diminishes progressively towards the periphery of the retina. Thus the colour photoreceptors—the cones for red, green and possibly also blue—have their greatest density of 150,000 per square mm at the foveola, which measures only 300–330 µm across.

 

Xanthophyll pigment

The optical system of the human eye is such that ambient light tends to fall with peak intensity on the macular area of the retina with much less on the retinal periphery. It must be significant therefore that not only is melanin more abundant in the macular region because its RPE cells are taller and more numerous per unit area than elsewhere30 but there is also in the retina’s central area the yellow pigment xanthophyll (Greek: ξάνθος xanthos, yellow). In this region of the retina, xanthophyll permeates all layers of the neurosensory retina between its two limiting membranes and is concentrated in the retinal cells, both the neurons and the supporting tissue cells. Recently attention has been drawn to the presence of a collection of retinal supporting tissue cells (called Müller cells after the person who first described them) over the internal surface of the fovea and forming a cone whose apex plugs the foveolar depression.

Retinal xanthophyll is a carotenoid, chemically related to vitamin A, whose absorption spectrum peaks at about 460 nm and ranges from 480 nm down to 390 nm It helps to protect the neurosensory retina by absorbing much of the potentially damaging shorter wavelength visible light, i.e. blue and violet, which is more scattered by small molecules and structures.

 

The blind spot

Because of the retina’s inverted arrangement, the axons (nerve fibres) transmitting data to the brain pass under cover of the retina’s inner surface to converge to a small area which is the optic nerve head, where they all exit the eye together as the optic nerve. The optic nerve head has no photoreceptors and so is blind, thereby producing a small blind spot in the visual field. No surprise, evolutionists criticized that. As Williams puts it:

‘Our retinal blind spots rarely cause any difficulty, but rarely is not the same as never. As I momentarily cover one eye to ward off an insect, an important event might be focused on the blind spot of the other.’ 3
Notwithstanding, this issue has to be viewed in perspective: the blind spot is centred at 15° away from the visual axis (3.7 mm from the foveola) and is very small in relation the visual field of an eye, occupying less than 0.25%. As mentioned above, the further away a point in the retina is from the foveola, the less will be its VA and its sensitivity. The retina surrounding the optic nerve head, in the light-adapted state, has a VA of only about 15% of that at the foveola. We can safely infer that the theoretical risk referred to by Williams arising from the blind spot in a one-eyed person, is negligible; and, in keeping with this, it is considered safe for a one-eyed person to drive a private motor car, i.e. for non-vocational purposes.’ 

Because the two visual fields overlap to a large degree, the blind spot of one eye is covered by the other eye’s visual field. It is true that occlusion or loss of one eye is a handicap, but this is not because of the blind spot of the seeing eye for the reasons given above.

 

Invertebrated eyes

Some claims that the verted retinae of cephalopods, such as squids and octopuses, are more efficient than the inverted retinae found in vertebrates. But this presupposes that the inverted retina is inefficient in the first place, and we’ve seen that isn’t the case. Also, they have never shown that cephalopods actually see better. On the contrary, their eyes merely ‘approach some of the lower vertebrate eyes in efficiency’ and they are probably colour blind. Further, the cephalopod retina, besides being ‘verted’, is actually much simpler than the ‘inverted’ retina of vertebrates; as Budelmann states, ‘The structure of the [cephalopod] retina is much simpler than in the vertebrate eye, with only two neural components, the receptor cells and efferent fibres’.5 It is an undulating structure with ‘long cylindrical photoreceptor cells with rhabdomeres consisting of microvilli’, so that the cephalopod eye has been described as a ‘compound eye with a single lens’. Finally, they live in regions with much lower light intensity than most vertebrates, which contributes to show that cephalopods eyes don’t need to be so complex as it’s usually claimed.

Despite the efforts of evolution promoters, the inverted retina isn’t an evidence of bad design; all the way around, even its “backwards wired” design poses a clear sign of planned origin, as to suit the demands of each living being, in accordance to its environment.

(From the article:  Is our ‘inverted’ retina really ‘bad design’?-Creation Ministries)

 

God bless you!

 

References

 

1 Dawkins, R., The Blind Watchmaker: Why the evidence of evolution reveals a universe without design. W.W. Norton and Company, New York, p. 93, 1986

2 Duke-Elder, S., System of Ophthalmology, Henry Kimpton, London, vol. 1, p. 147, 1958.

3 Parver, L.M., Auker, C., Carpenter, D.O., Choroidal blood flow as a heat dissipating mechanism in the macula, Am. J. Ophthalmol. 89:641–646, 1980.

4 Williams, G.C., Natural Selection: Domains, Levels and Challenges, Oxford University Press, Oxford, pp. 72–73, 1992.

5 Budelmann, B.U., Cephalopod sense organs, nerves and brain, 1994. In Pörtner, H.O., O’Dor, R.J. and Macmillan, D.L., ed., Physiology of cephalopod molluscs: lifestyle and performance adaptations, Gordon and Breach, Basel, Switzerland, p. 15, 1994.

Explain that, evolutionists…

Details…

Evolutionists forges so many theories and wishful thinking, trying to (naturalistic) explaining how a organism ‘evolved’ from a simpler, incomplete form to a fully formed one.. But they don’t explain the details, surely because these make the supposed probability of evolution to occur even smaller (If it had actually any possibility to occur!)

Darwin himself found amazing and quite improbable for an eye to have evolved through minute developments, improvements, during millions of years.. Let alone if he actually knew about that:

 

Biochemical sketch of the eye’s operation:

When light first strikes the retina a photon interacts with a molecule
called 11-cis-retinal, which rearranges within picoseconds to trans-retinal.
(A picosecond is about the time it takes light to
travel the breadth of a single human hair.) The change in the shape of
the retinal molecule forces a change in the shape of the protein, rhodopsin,
to which the retinal is tightly bound. The protein’s metamorphosis alters
its behavior. Now called metarhodopsin II, the protein sticks to another
protein, called transducin. Before bumping into metarhodopsin II,
transducin had tightly bound a small molecule called GDP. But when
transducin interacts with metarhodopsin II, the GDP falls off, and a
molecule called GTP binds to
transducin. (GTP is closely related to, but critically different from, GDP.)

GTP-transducin-metarhodopsin II now binds to a protein called
phosphodiesterase, located in the inner membrane of the cell. When
attached to metarhodopsin II and its entourage, the phosphodiesterase
acquires the chemical ability to «cut» a molecule called cGMP (a chemical
relative of both GDP and GTP). Initially there are a lot of cGMP molecules
in the cell, but the phosphodiesterase lowers its concentration, just as a
pulled plug lowers the water level in a bathtub.

Another membrane protein that binds cGMP is called an ion channel.
It acts as a gateway that regulates the number of sodium ions in the cell.
Normally the ion channel allows sodium ions to flow into the cell, while
a separate protein actively pumps them out again. The dual action of the
ion channel and pump keeps the level of sodium ions in the cell within a
narrow range. When the amount of cGMP is reduced because of cleavage
by the phosphodiesterase, the ion channel closes, causing the cellular
concentration of positively charged sodium ions to be reduced. This causes
an imbalance of charge across the cell membrane that, finally, causes a
current to be transmitted down the optic nerve to the brain. The result,
when interpreted by the brain, is vision.

If the reactions mentioned above were the only ones that operated in
the cell, the supply of 11-cis-retinal, cGMP and sodium ions would quickly
be depleted. Something has to turn off the proteins that were turned on
and restore the cell to its original state. Several mechanisms do this. First,
in the dark the ion channel (in addition to sodium ions) also lets calcium
ions into the cell. The calcium is pumped back out by a different protein so
that a constant calcium concentration is maintained. When cGMP levels
fall, shutting down the ion channel, calcium ion concentration decreases,
too. The phosphodiesterase enzyme, which destroys cGMP slows down at
lower calcium concentration. Second, a protein called guanylate cyclase
begins to resynthesize cGMP when calcium levels start to fall. Third,
while all of this is going on, metarhodopsin II is chemically modified by
an enzyme called rhodopsin kinase. The modified rhodopsin then binds to
a protein known as arrestin, which prevents the rhodopsin from activating
more transducin. So the cell contains mechanisms to limit the amplified
signal started by a single photon.

Trans-retinal eventually falls off of rhodopsin and must be reconverted
to 11-cis-retinal and again bound by rhodopsin to get back to the starting
point for another visual cycle. To accomplish this, trans-retinal is first
chemically modified by an enzyme to trans-retinol—a form containing
two more hydrogen atoms. A second enzyme then converts the molecule
to 11-cis-retinol. Finally, a third enzyme removes the previously added
hydrogen atoms to form 11-cis-rennal, a cycle is complete. .

BEETLE BOMBS

The bombardier beetle is an insect of unassuming appearance,
measuring about one half-inch in length. When it is threatened by another
bug, however, the beetle has a special method of defending itself, squirting
a boiling-hot solution at the enemy out of an aperture in its hind section.16
The heated liquid scalds its target, which then usually makes other plans
for dinner. How is this trick done?

It turns out that the bombardier beetle is using chemistry. Prior to battle,
specialized structures called secretory lobes make a very concentrated
mixture of two chemicals, hydrogen peroxide and hydroquinone.
The hydrogen peroxide is the same material as one can buy in a
drugstore; hydroquinone is used in photographic development. The
mixture is sent into a storage chamber called the collecting vesicle.
The collecting vesicle is connected to, but ordinarily sealed off from, a
second compartment called (evocatively) the explosion chamber. The
two compartments are kept separate from one another by a duct with a
sphincter muscle, much like the sphincter muscles upon which humans
depend for continence. Attached to the explosion chamber are a number
of small knobs called ectodermal glands; these secrete enzyme catalysts
into the explosion chamber. When the beetle feels threatened it squeezes
muscles surrounding the storage chamber while simultaneously relaxing
the sphincter muscle. This forces the solution of hydrogen peroxide and
hydroquinone to enter the explosion chamber, where it mixes with the
enzyme catalysts.

Now, chemically, things get very interesting. The hydrogen peroxide
rapidly decomposes into ordinary water and oxygen, just as a store-bought
bottle of hydrogen peroxide will decompose over time if left open. The
oxygen reacts with the hydroquinone to yield more water, plus a highly
irritating chemical called quinone. These reactions release a large quantity
of heat. The temperature of the solution rises to
the boiling point; in fact, a portion vaporizes into steam. The steam
and oxygen gas exert a great deal of pressure on the walk of the explosion
chamber. With the sphincter muscle now closed, a channel leading outward
from the beetle’s body provides the only exit for the boiling mixture.
Muscles surrounding the channel allow the steam jet to be directed at the
source of danger. The end result is that the beetle’s enemy is scalded by a
steaming solution of the toxic chemical quinone.

You may wonder why the mixture of hydrogen peroxide and quinone
did not react explosively when they were in the collecting vesicle. The
reason is that many chemical reactions occur quite slowly if there is no
easy way for the molecules to get together on the atomic level—otherwise,
even a book would burst into flame as it reacted with oxygen in the air. As
an analogy, consider a locked door. There is no easy way for people on opposite sides of the door to get together, even
if they would wanted to do so. If someone has the key, however, then the
door can be opened and proper introductions can be made. The enzyme
catalysts play the role of the key, allowing the hydrogen peroxide and hydroquinone to get together
on the atomic level so that a reaction can take place.

The cascade

The body commonly stores enzymes (proteins that catalyze a chemical
reaction, like the cleavage of fibrinogen) in an inactive form for later use.
The inactive forms are called proenzymes. When a signal is received that
a certain enzyme is needed, the corresponding proenzyme is activated to
give the mature enzyme. As with the conversion of fibrinogen to fibrin,
proenzymes are often activated by cutting off a piece of the proenzyme
that is blocking a critical area. The strategy is commonly used with
digestive enzymes. Large quantities can be stored as inactive proenzymes,
then quickly activated when the next good meal comes along.

Thrombin initially exists as the inactive form, prothrombin. Because it
is inactive, prothrombin can’t cleave fibrinogen, and the animal is saved
from death by massive, inappropriate clotting. Still, the dilemma of control
remains. If the cartoon saw were inactivated, the telephone pole would not
fall at the wrong time. If nothing switches on the saw, however, then it
would never cut the rope; the pole wouldn’t fall even at the right time. If
fibrinogen and prothrombin were the only proteins in the blood-clotting
pathway, again our animal would be in bad shape. When the animal
was cut, prothrombin would just float helplessly by the fibrinogen as the
animal bled to death. Because prothrombin cannot cleave fibrinogen to
fibrin, something is needed to activate prothrombin.

Perhaps the reader can see why the blood-clotting system is called a
cascade—a system where one component activates another component,
which activates a third component, and so on.

A protein called Stuart factor cleaves prothrombin, turning it into active
thrombin that can then cleave fibrinogen to fibrin to form the blood clot.
Unfortunately, as you may have guessed, if Stuart factor, prothrombin,
and fibrinogen were the only blood-clotting proteins, then Stuart factor
would rapidly trigger the cascade, congealing all the blood of the organism. So Stuart factor also exists in an inactive
form that must first be activated.

At this point there’s a little twist to our developing chicken-and-egg
scenario. Even activated Stuart factor can’t turn on prothrombin. Stuart
factor and prothrombin can be mixed in a test tube for longer than it would
take a large animal to bleed to death without any noticeable production
of thrombin. It turns out that another protein, called accelerin, is needed
to increase the activity of Stuart factor. The dynamic duo—accelerin
and activated Stuart factor— cleave prothrombin fast enough to do the
bleeding animal some good. So in this step we need two separate proteins
to activate one proenzyme.

Yes, accelerin also initially exists in an inactive form, called proaccelerin
(sigh). And what activates it? Thrombin! But thrombin, as we have seen,
is further down the regulatory cascade than proaccelerin. So thrombin
regulating the production of accelerin is like having the granddaughter
regulate production of the grandmother. Nonetheless, due to a very low
rate of cleavage of prothrombin by Stuart factor, it seems there is always
a trace of thrombin in the bloodstream. Blood clotting is therefore auto-
catalytic, because proteins in the cascade accelerate the production of
more of the same proteins.

We need to back up a little at this point because, as it turns out,
prothrombin as it is initially made by the cell can’t be transformed into
thrombin, even in the presence of activated Stuart factor and accelerin.
Prothrombin must first be modified by having
ten specific amino acid residues, called glutamate (Glu) residues, changed
to «.-carboxyglutamate (Gla) residues. The modification can be compared
to placing a lower jaw onto the upper jaw of a skull. The completed
structure can bite and hang on to the bitten object; without the lower jaw,
the skull couldn’t hang on. In the case of prothrombin, Gla residues «bite»
(or bind) calcium, allowing prothrombin to stick to the surfaces of cells.
Only the intact, modified calcium-prothrombin complex, bound to a cell
membrane, can be cleaved by activated Stuart factor and accelerin to give
thrombin.

The modification of prothrombin does not happen by accident. Like
virtually all biochemical reactions, it requires catalysis by a specific enzyme. In addition to the enzyme, however, the conversion of Glu
to Gla needs another component: vitamin K. Vitamin . is not a protein;
rather, it is a small molecule, like the 11-cis-retinal
that is necessary for vision. Like a gun that needs bullets, the enzyme that
changes Glu to Gla needs vitamin . to work. One type of rat poison is
based on the role that vitamin . plays in blood coagulation. The synthetic
poison, called «warfarin» (for the Wisconsin Alumni Research Fund,
which receives a cut of the profits from its sale), was made to look like
vitamin . to the enzyme that uses it. In the presence of warfarin the
enzyme is unable to modify prothrombin. When rats eat food poisoned
with warfarin, prothrombin is neither modified nor cleaved, and the
poisoned animals bleed to death.

But it still seems we haven’t made much progress—now we have to
go back and ask what activates Stuart factor. It turns out that it can be
activated by two different routes, called the intrinsic and the extrinsic
pathways. In the intrinsic pathway, all the proteins required for clotting
are contained in the blood plasma; in the extrinsic pathway, some clotting
proteins occur on cells. Let’s first examine the intrinsic pathway

When an animal is cut, a protein called Hageman factor sticks to the
surface of cells near the wound. Bound Hageman factor is then cleaved by
a protein called HMK to yield activated Hageman factor. Immediately the
activated Hageman factor converts another protein, called prekallikrein, to
its active form, kallikrein. Kallikrein helps HMK speed up the conversion
of more Hageman factor to its active form. Activated Hageman factor
and HMK then together transform another protein, called …, to its
active form. Activated … in turn, together with the activated form of
another protein (discussed below) called convertin, switch a protein called
Christmas factor to its active form. Finally, activated Christmas factor,
together with antihemophilic factor (which is itself activated by thrombin
in a manner similar to that of proaccelerin) changes Stuart factor to its
active form.

Like the intrinsic pathway, the extrinsic pathway is also a cascade. The
extrinsic pathway begins when a protein called proconvertin is turned
into convertin by activated Hageman factor and thrombin. In the presence
of another protein, tissue factor, convertin changes Stuart factor to its active form. Tissue factor, however, only appears on the outside of cells that are usually not in contact with blood.

Therefore, only when an injury brings tissue into contact with blood
will the extrinsic pathway be initiated. (A cut plays a role similar to that
of Foghorn Leghorn picking up the dollar. It is the initiating event—
something outside of the cascade mechanism itself.)

The intrinsic and extrinsic pathways cross over at several points.
Hageman factor, activated by the intrinsic pathway, can switch on
proconvertin of the extrinsic pathway. Convertin can then feed back
into the intrinsic pathway to help activated … activate Christmas
factor. Thrombin itself can trigger both branches of the clotting cascade
by activating antihemophilic factor, which is required to help activated
Christmas factor in the conversion of Stuart factor to its active form, and
also by activating proconvertin. .

 

IT’S NOT OVER YET
Once clotting has begun, what stops it from continuing until all the blood in the animal has solidified? Clotting is confined to the site of injury in several ways. First, a plasma protein called antithrombin binds to the active (but not the inactive) forms of most clotting proteins and inactivates them. Antithrombin is itself relatively inactive, however, unless it binds to a substance called heparin. Heparin occurs inside cells and undamaged blood vessels. A second way in which clots are localized is

through the action of protein C. After activation by thrombin, protein С destroys accelerin and activated antihemophilic factor. Finally, a protein called thrombomodulin lines the surfaces of the cells on the inside of blood vessels. Thrombomodulin binds thrombin, making it less able to cut fibrinogen and simultaneously increasing its ability to activate protein C.
When a clot initially forms, it is quite fragile: if the injured area is bumped the clot can easily be disrupted, and bleeding starts again. To prevent this, the body has a method to strengthen a clot once it has formed. Aggregated fibrin is «tied together» by an activated protein called FSF (for «fibrin stabilizing factor»), which forms chemical cross-links between different fibrin molecules. Eventually, however the blood clot must be removed after wound healing has progressed. A protein called plasmin acts as a scissors specifically to cut up fibrin clots. Fortunately, plasmin does not work on fibrinogen. Plasmin cannot act too quickly, however, or the wound wouldn’t have sufficient time to heal completely. It therefore occurs initially in an inactive form called plasminogen. Conversion of plasminogen to plasmin is catalyzed by a protein called t-PA.

There are also other proteins that control clot dissolution, including α2-antiplasmin, which binds to plasmin, preventing it from destroying fibrin clots.

 
We could also describe many other wonderful systems and processes of organisms, such as the biochemical structure of a bacterium cilium, the cell structure, made up of 20 types of amino acids L-handed, thousands of proteins, billions of DNA genes, the “deliver system” of our organism, lymphatic system, nervous system, etc.. The more the science advances in its discoveries, the more it’s proven that the nature and Universe to be both designed in its minimal details.

 

From: Michael Behe’s book, Darwin’s Black Box..

God bless you!

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