Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


You are not connected. Please login or register

Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias »  The nitrogen cycle, irreducible interdependence, and the origin of life

The nitrogen cycle, irreducible interdependence, and the origin of life

View previous topic View next topic Go down  Message [Page 1 of 1]

Admin


Admin
The nitrogen cycle, irreducible interdependence, and the origin of life

http://reasonandscience.heavenforum.org/t1562-the-nitrogen-cicle-irreducible-interdependence-and-the-origin-of-life

Nitrogen is one of the essential nutrients of life on Earth, with some organisms, such as the kinds of microbes found within the roots of legume plants, capable of converting nitrogen gas into molecules that other species can use. 1 Nitrogen fixation, as the process is called, involves breaking the powerful chemical bonds that hold nitrogen atoms in pairs in the atmosphere and using the resulting single nitrogen atoms to help create molecules such as ammonia, which is a building block of many complex organic molecules, such as proteins, DNA and RNA. Stüeken developed a model of abiotic nitrogen processes that could have played a role in early Earth. The results showed that such abiotic processes alone could not explain the nitrogen levels seen in the Isua rocks. 


Nitrogen is a part of vital organic compounds in microrganisms, such as amino acids, proteins and DNA. During the conversion of nitrogen, cyanobacterias will first convert nitrogen from the atmosphere into ammonia and ammonium through nitrogenase, during the nitrogen fixation process. After ammonium fixation, the ammonia and ammonium that is formed convert it through further reduction to nitrite and nitrage into their cellular material, and on dying, decompose and make nitrogen available to the soil,  which serves plants for nutrition, after which they are converted into nitrogen-containing organic molecules, such as amino acids and DNA. Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals.

So, resuming :  Without cyanobacteria - no fixed nitrogen is available. Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised. Without DNA, no amino-acids,protein, or cyanobacteria are possible. So there you have a interdependent cycle, with no beginning. But, wait : there is more : cyanobacteria are facultative anaerobes - meaning that they can respire either aerobically or anaerobically. The complexity of two respiratory cycles is very high: the Krebs cycle alone requiring about 12 enzymes, and the anaerobic requiring somewhat fewer, say 8.  So in order for the cyanobacteria to survive, about 40 enzymes are already involved - none of which can be made without fixed nitrogen. So here we have a chicken-egg problem par excellence , which came first..... ??

 Lighting is another source, but since its supposed that Photosynthesis had not evolved at the stage of a common ancestor, there was a reduced atmosphere without oxygen. If there was a reduced atmosphere ( which btw. there is no scientific evidence for, rather the oposit is the case ) then there would be no ozone layer, and  the ultraviolet radiation would penetrate the atmosphere and would destroy the amino acids as soon as they were formed. If the Cyanobacterias however would overcome that problem ( its supposed the bacterias in the early earth lived in the water, but that would draw other unsurmountable problems ), and evolve photosynthesis, they would have to evolve at the same time protective enzymes that prevented them oxygen to damage their DNA through hydroxyl radicals. So what evolutionary advantage would there be they to do this ?

 To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet?  The explanations are fantasious at best.  But even if lets say that enough nitrogen would be available at the primordial earth , that far from explains the information encoded in Fifteen nitrogen fixation or nitrogen fixation-related genes, including the structural genes for nitrogenase,nifHDK, which are clustered together as follows:nifB-fdxN-nifS-nifU-nifH-nifD- nifK-nifE-nifN-nifX-orf2-nifW-hesA-hesB-fdxH.Thesegenes are organized in at least six transcriptional units:nifB-fdxN-nifS-nifU, nifHDK, nifEN,nifX-orf2, nifW-hesA-hesB, and fdxH.......  
http://www.ps-19.org/Crea06EcoSys/index.html

"Today, large amounts of nitrate are made when oxygen and nitrogen combine during lightening storms, but this could not happen in the early oxygen-deficient atmosphere.... The scarcity of ammonia and nitrate posed a major problem to life." Also see NAS studies]

Without cyanobacteria - not enough fixed nitrogen is available.

Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised.

Without DNA, no amino-acids,protein, or cyanobacteria are possible.

Thats called a interdependent system. It cannot have evolved in small steps. All must exist at once.


Nitrogen cycle

Nitrogen is a part of vital organic compounds in microrganisms, such as amino acids, proteins and DNA. The gaseous form of nitrogen (N2), makes up 78% of the troposphere. One might think this means we always have plenty of nitrogen available, but unfortunately it does not work that way. Nitrogen in the gaseous form cannot be absorbed and used as a nutrient by plants and animals; it must first be converted by nitrifying bacteria, so that it can enter food chains as a part of the nitrogen cycle.

During the conversion of nitrogen cyano bacteria will first convert nitrogen into ammonia and ammonium, during the nitrogen fixation process. Plants can use ammonia as a nitrogen source.

Nitrogen fixation is carried out according to the following reaction:
N2 + 3 H2 -> 2 NH3

After ammonium fixation, the ammonia and ammonium that is formed will be transferred further, during the nitrification process. Aerobic bacteria use oxygen to convert these compounds. Nitrosomonas bacteria first convert nitrogen gas to nitrite (NO2-) and subsequently nitrobacter convert nitrite to nitrate (NO3-), a plant nutrient.

Nitrification is carried out according to the following reactions:
2 NH3 + 3O2 - > 2 NO2 + 2 H+ + 2 H2O
2 NO2- + O2 -> 2 NO3-

Plants absorb ammonium and nitrate during the assimilation process, after which they are converted into nitrogen-containing organic molecules, such as amino acids and DNA.
Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals.
When nitrogen nutrients have served their purpose in plants and animals, specialized decomposing bacteria will start a process called ammonification, to convert them back into ammonia and water-soluble ammonium salts. After the nutrients are converted back into ammonia, anaerobic bacteria will convert them back into nitrogen gas, during a process called denitrification.

Denitrification is carried out according to the following reaction:
NO3- + CH2O + H+ -> ½ N2O + CO2 + 1½ H2O

Finally, nitrogen is released into the atmosphere again. The whole process starts over after release.

A schematic representation of the nitrogen cycle is shown here:

Read more: http://www.lenntech.com/nitrogen-cycle.htm#ixzz2uctBKbvK




Nitrogen as a limiting factor

Although the nitrogen conversion processes often occurs and large quantities of plant nutrients are produced, nitrogen is often a limiting factor for plant growth. Water flowing across the soil causes this error. Nitrogen nutrients are water-soluble and as a result they are easily drained away, so that they are no longer available for plants.

The annamox reaction

In 1999 researchers at the Gist-Brocades in Delft, The Netherlands, discovered a new reaction to be added to the nitrogen cycle; the so-called annamox reaction. This is now found to occur in the Black Sea, as well. The reaction implies conversion of nitrite and ammonium to pure nitrogen gas (N2), which than escapes to the atmosphere. The reaction mechanism is triggered by a newly discovered bacterium, called Brocadia anammoxidans. This appears to be a compartmentalized bacterium; within the cell membrane two compartments can be found which are also surrounded by a membrane, a very rare phenomenon. Intermediate products of the reaction included hydroxylamine, and toxic hydrazine compounds. The bacterial membranes were found to consists of badly permeable membranes, which are thought to function as a barrier for hydrazines produced within the cell. This discovery has major consequences, as it alters the entire contribution of oceans to the nitrogen balance.




Could the oxygen and nitrogen cicle be explained by naturalistic means ? The reason for the abundance of oxygen in the atmosphere is the presence of a very large number of organisms which produce oxygen as a byproduct of their metabolism. Cyanobacteria or blue-green algae became the first microbes to produce oxygen by photosynthesis. They are one of the oldest bacteria that live on earth, said to exist perhaps as long as 3.5 billion years. And their capabilities are nothing more than astounding. No cianobacteria, no oxygen, no higher life forms. These cianobacterias have incredibly sophisticated enzyme proteins and metabolic pathways, like the electron transport chains, ATP synthase motors, circadian clock, the photosynthetic light reactions, carbon concentration mechanism, and transcriptional regulation , they produce binded nitrogen through nitrogenase, a highly sophisticated mechanism to bind nitrogen, used as a nutrient for plant and animal growth.

The Nitrogen cycle is a lot more complex than the carbon cycle. Nitrogen is a very important element. It makes up almost 80% of our atmosphere, and it is an important component of proteins and DNA, both of which are the building blocks of animals and plants. Therefore without nitrogen we would lose one of the most important elements on this planet, along with oxygen, hydrogen and carbon. There are a number of stages to the nitrogen cycle, which involve breaking down and building up nitrogen and it’s various compounds.There is no real starting point for the nitrogen cycle. It is an endless cycle. Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone. It must have a degree of specificity that in all probability could not have been produced by chance. A given function or step in the system may be found in several different unrelated organisms. The removal of any one of the individual biological steps will resort in the loss of function of the system. The data suggest that the nitrogen cycle may be irreducibly interdependent based on the above criteria. No proposed neo-Darwinian mechanisms can explain the origin of such a system.The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. Its needed by all living things to build proteins and nucleic acids.

This is one of the hardest chemical bonds of all to break. So, how can nitrogen be brought out of its tremendous reserves in the atmosphere and into a state where it can be used by living things? To be metabolically useful, atmospheric nitrogen must be reduced. It must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them. This process, known as nitrogen fixation, occurs through lightening, but most in certain types of bacteria, namely cianobacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N≡N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation). Nitrogenase is a very complex enzyme system. Nitrogenase genes are distributed throughout the prokaryotic kingdom, including representatives of the Archaea as well as the Eubacteria and Cyanobacteria.With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision.

In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism, but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue. ‘Nature is really good at it (nitrogen-splitting), so good in fact that we've had difficulty in copying chemically the essence of what bacteria do so well.’ If one merely substitutes the name of God for the word 'nature', the real picture emerges.These proteins use a collection of metal ions as the electron carriers that are responsible for the reduction of N2 to NH3. All organisms can then use this reduced nitrogen (NH3) to make amino acids. In humans, reduced nitrogen enters the physiological system in dietary sources containing amino acids. One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering.Without cyanobacteria - no fixed nitrogen is available.Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised. Without DNA, no amino-acids,protein, or cyanobacteria are possible. So thats a interdependent system.

In short :

The short argument :

Without cyanobacteria - not enough fixed nitrogen is available.

Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised.

Without DNA, no amino-acids,protein, or cyanobacteria are possible.

Thats called a interdependent system. It cannot have evolved in small steps. All must exist at once.




http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/NitrogenCycle.html

http://www.grisda.org/origins/60006.pdf

he nitrogen cycle, incorporating a broad
spectrum of unconsciously cooperating species, operates in a coordinated
assembly-line manner that is extraordinary and impressive.

A relatively small, but not insignificant, amount of nitrogen is fixed by
lightning passing through the atmosphere.

1C. DOES ATMOSPHERIC NITROGEN FIXATION BRIDGE BIOLOGICAL
FIXATION?


Because nitrates can be produced in the absence of biological nitrogen
fixation, it might be tempting to suggest that this biological step in the
nitrogen cycle is dispensable. In real life this is not the case because of
three factors: 1) Nitrates from atmospheric fixation must be reduced to
ammonia if they are to be biologically useful. 2) Electric storms and other
causes of atmospheric fixation are more common in some places than
others so nitrate produced by this means is irregularly distributed. 3) The
amount of nitrogen fixed by thermal shock is comparatively small, so this
method cannot be considered either consistent or sufficient in itself to
sustain life as it is now.

Atmospheric nitrogen fixation could not have been part of a bootstrap
mechanism by which life originated because its product, nitrate, is not
directly biologically useful. In addition, an abiotic mechanism to convert
nitrate to biologically useful forms like ammonia is unavailable to bridge
the gap between the products of atmospheric and biological fixation. There
are no shared enzymes between biological nitrogen fixation and assimilation,
even though their end product — ammonia — is the same. As a conse-
quence, one cannot be explained as a relatively simple adaptation of the
other to a different task.



Most arguments for evolution of the nitrogen cycle allow for the existence
of life before a complete nitrogen cycle existed, but some source
of nitrogen in the right form is required for life to exist. This is a major problem.

The nitrogen cycle requirse atmospheric nitrogen, an energy source (typically photosynthesis), and
enzymatic facilitation. Photosynthesis also provides carbon skeletons
for amino acids which are aminated using nitrogen fixed in the nitrogen
cycle. These amino acids serve in turn as building blocks of the enzymes
and other proteins involved in both photosynthesis and the nitrogen cycle.
In addition, amino acids provide the nitrogen found in nucleotides which
are central to energy metabolism and serve as the building blocks of both
DNA and RNA. Ultimately, protein enzymes mediate the manufacture of
all biological macromolecules. Thus, all the vital processes found in living
things are interdependently linked via the nitrogen cycle.


How nitrates could have been abiotically modified to form biologically
useful compounds is unclear. Even if the energy needed for nitrogen fixation
or assimilation did not come from photosynthesis or chemosynthesis,
some energy source is still required. In addition, enzymes that mediate the
necessary reactions are also required. It may be possible to build a bypass
around photosynthesis, but it is not clear that this would provide a more
plausibly evolved pathway. No matter what the mechanism, complex
protein catalysts appear to be required and production of these requires
the ultimate products of nitrogen fixation — amino acids and nucleotides.

herefore, the formation of nitrate as a result of atmospheric nitrogen fixation notwithstanding, life
itself appears unlikely to have originated in an oxidizing atmosphere and
lightning-induced nitrate production seems improbable as a source of bio-
logically useful nitrogen during alleged evolution of nitrogen fixation
systems. In an oxidizing atmosphere, life — if it already existed — must
have possessed systems to deal with damage caused by toxic byproducts
of atmospheric nitrogen fixation, but life is unlikely to have evolved in the
first place due to the impact of some of these byproducts.

Atmospheric nitrogen fixation could not have been part of a bootstrap
mechanism by which life originated because its product, nitrate, is not
directly biologically useful. In addition, an abiotic mechanism to convert
nitrate to biologically useful forms like ammonia is unavailable to bridge
the gap between the products of atmospheric and biological fixation. There
are no shared enzymes between biological nitrogen fixation and assimilation,
even though their end product — ammonia — is the same.


As a consequence, one cannot be explained as a relatively simple adaptation of the
other to a different task. In organisms living today, biological nitrogen fixation
requires photosynthesis or chemo synthesis to provide both energy and carbon
backbones for amination to produce amino acids. Of particular significance, both
photosynthesis and chemosynthesis require nitrogen-containing proteins;
thus, in these organisms a chicken-or-egg conundrum exists which atmospheric
nitrogen fixation does not solve


How nitrates could have been abiotically modified to form biologically
useful compounds is unclear. Even if the energy needed for nitrogen fixation
or assimilation did not come from photosynthesis or chemosynthesis,
some energy source is still required. In addition, enzymes that mediate the
necessary reactions are also required. It may be possible to build a bypass
around photosynthesis, but it is not clear that this would provide a more
plausibly evolved pathway. No matter what the mechanism, complex
protein catalysts appear to be required and production of these requires
the ultimate products of nitrogen fixation — amino acids and nucleotides.

The formation of nitrate as a result of atmospheric nitrogen fixation notwithstanding,
life itself appears unlikely to have originated in an oxidizing atmosphere and lightning-
induced nitrate production seems improbable as a source of biologically useful nitrogen
during alleged evolution of nitrogen fixation systems. In an oxidizing atmosphere, life
if it already existed — must have possessed systems to deal with damage caused by
toxic byproducts of atmospheric nitrogen fixation, but life is unlikely to have evolved
in the first place due to the impact of some of these byproducts.


Any reduced organic molecules must be protected in some way from O3
and other free radicals produced as a byproduct of
atmospheric fixation. In either scenario, production of life and evolution
of biological nitrogen fixation present conundrums that the neo-Darwinian
mechanism does not reasonably resolve.

While any number of scenarios may be suggested to overcome these
issues, none actually solves the problems using strictly Darwinian principles.
Take the following scenario for example: life evolves in a reducing
atmosphere which subsequently changes to an oxidizing atmosphere. Under
these new circumstances, bacteria among the few organisms that survived
the change evolve the ability to use nitrogen in nitrate thus evolving assimi-
lation before biological nitrogen fixation. Life is sustained by atmospheric
fixation until biological nitrogen fixation evolves. Problems with this scenario
include: 1) It assumes that assimilation is evolvable and had evolved enough
before it was vital to sustain some bacteria that also had the ability to
survive an oxidizing atmosphere; 2) it assumes atmospheric fixation at
levels sufficient to sustain life, but not so rapid that nitrate accumulated to
the point that it caused problems; 3) evidence is lacking for a reducing
atmosphere; 4) the concurrent need to develop a means of aminating
carbon skeletons to produce amino acids; 5) the concurrent need to deal
with radicals produced as part of the process; 6) availability of energy
resources and reducing power sufficient to allow assimilation to work
and so on. Probably the most troubling assumption is that any organism
adapted to living in a reducing environment could survive the transition to
an oxidizing environment. Ultimately scenarios of this kind simply split a
single big problem into two big problems for Darwinism to explain; they
do not reduce the problem to small steps that unguided nature might reason-
ably be expected to take via the neo-Darwinian process. In addition, they
do not explain biological nitrogen fixation, but instead invoke a different
biological means of obtaining nitrogen without addressing the point about
nitrogen fixation.

Unquestionably, biological nitrogen fixation is no simple process and
a design argument could be made based on this single step in the nitrogen
cycle. It is unlikely to have been produced via a step-by-step Darwinian
process because nitrogenase itself is immensely complex, requires auxiliary
complex mechanisms to maintain low oxygen tension, and also needs
reduced carbon backbones as substrates for amination to store ammonia
as glutamine.

Nitrogen is arguably the most important nutrient in regulating primary productivity and species diversity in both aquatic and terrestrial ecosystems (Vitousek et al. 2002). Microbially-driven processes such as nitrogen fixation, nitrification, and denitrification, constitute the bulk of nitrogen transformations, and play a critical role in the fate of nitrogen in the Earth's ecosystems.

http://archive.bio.ed.ac.uk/jdeacon/microbes/nitrogen.htm

Microorganisms have a central role in almost all aspects of nitrogen availability and thus for life support on earth:

      some bacteria can convert N2 into ammonia by the process termed nitrogen fixation; these bacteria are either free-living or form symbiotic associations with plants or other organisms (e.g. termites, protozoa)
      other bacteria bring about transformations of ammonia to nitrate, and of nitrate to N2 or other nitrogen gases
      many bacteria and fungi degrade organic matter, releasing fixed nitrogen for reuse by other organisms.




http://www.nature.com/scitable/knowledge/library/the-nitrogen-cycle-processes-players-and-human-15644632

Nitrogen Fixation


In addition to N2 and NH3, nitrogen exists in many different forms, including both inorganic (e.g., ammonia, nitrate) and organic (e.g., amino and nucleic acids) forms. Thus, nitrogen undergoes many different transformations in the ecosystem, changing from one form to another as organisms use it for growth and, in some cases, energy. The major transformations of nitrogen are nitrogen fixation, nitrification, denitrification, anammox, and ammonification (Figure 1). The transformation of nitrogen into its many oxidation states is key to productivity in the biosphere and is highly dependent on the activities of a diverse assemblage of microorganisms, such as bacteria, archaea, and fungi.

N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms, and it requires a large amount of energy to break this bond. The whole process requires eight electrons and at least sixteen ATP molecules (Figure 2). As a result, only a select group of prokaryotes are able to carry out this energetically demanding process. Although most nitrogen fixation is carried out by prokaryotes, some nitrogen can be fixed abiotically by lightning or certain industrial processes, including the combustion of fossil fuels.

Although there is great physiological and phylogenetic diversity among the organisms that carry out nitrogen fixation, they all have a similar enzyme complex called nitrogenase that catalyzes the reduction of N2 to NH3 (ammonia), which can be used as a genetic marker to identify the potential for nitrogen fixation.




The process of converting N2 into biologically available nitrogen is called nitrogen fixation. N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms, and it requires a large amount of energy to break this bond. The whole process requires eight electrons and at least sixteen ATP molecules (Figure 2). As a result, only a select group of prokaryotes are able to carry out this energetically demanding process. Although most nitrogen fixation is carried out by prokaryotes, some nitrogen can be fixed abiotically by lightning or certain industrial processes, including the combustion of fossil fuels.

Nitrification

Nitrification is the process that converts ammonia to nitrite and then to nitrate and is another important step in the global nitrogen cycle. Most nitrification occurs aerobically and is carried out exclusively by prokaryotes. There are two distinct steps of nitrification that are carried out by distinct types of microorganisms. The first step is the oxidation of ammonia to nitrite, which is carried out by microbes known as ammonia-oxidizers. Aerobic ammonia oxidizers convert ammonia to nitrite via the intermediate hydroxylamine, a process that requires two different enzymes, ammonia monooxygenase


Energy generation in Nitrosomonas. Only two enzymes, ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO) are involved in the oxidation of ammonia to nitrite.

hydroxylamine oxidoreductase



Nitrite can be further acted on by another nitrifying bacteria, Nitrobacter. This microbe oxidizes nitrite to nitrate using oxygen as the terminal electron accepter. A proton gradient is established with resultant synthesis of ATP. Nitrobacter is often found in tandem with Nitrosomonas since the end product of Nitrosomonas metabolism is the energy substrate for Nitrobacter. This type of loose association is probably common in the environment and in this case benefits both organisms. Nitrobacter is provided with substrate and Nitrosomonas has its end product removed, which helps drive its metabolism.

and hydroxylamine oxidoreductase (Figure 4). The process generates a very small amount of energy relative to many other types of metabolism; as a result, nitrosofiers are notoriously very slow growers. Additionally, aerobic ammonia oxidizers are also autotrophs, fixing carbon dioxide to produce organic carbon, much like photosynthetic organisms, but using ammonia as the energy source instead of light.

Unlike nitrogen fixation that is carried out by many different kinds of microbes, ammonia oxidation is less broadly distributed among prokaryotes. Until recently, it was thought that all ammonia oxidation was carried out by only a few types of bacteria in the genera Nitrosomonas, Nitrosospira, and Nitrosococcus. However, in 2005 an archaeon was discovered that could also oxidize ammonia (Koenneke et al. 2005). Since their discovery, ammonia-oxidizing Archaea have often been found to outnumber the ammonia-oxidizing Bacteria in many habitats. In the past several years, ammonia-oxidizing Archaea have been found to be abundant in oceans, soils, and salt marshes, suggesting an important role in the nitrogen cycle for these newly-discovered organisms. Currently, only one ammonia-oxidizing archaeon has been grown in pure culture, Nitrosopumilus maritimus, so our understanding of their physiological diversity is limited.

The second step in nitrification is the oxidation of nitrite (NO2-) to nitrate (NO3-) (Figure 5). This step is carried out by a completely separate group of prokaryotes, known as nitrite-oxidizing Bacteria. Some of the genera involved in nitrite oxidation include Nitrospira, Nitrobacter, Nitrococcus, and Nitrospina. Similar to ammonia oxidizers, the energy generated from the oxidation of nitrite to nitrate is very small, and thus growth yields are very low. In fact, ammonia- and nitrite-oxidizers must oxidize many molecules of ammonia or nitrite in order to fix a single molecule of CO2. For complete nitrification, both ammonia oxidation and nitrite oxidation must occur.


Anammox

Traditionally, all nitrification was thought to be carried out under aerobic conditions, but recently a new type of ammonia oxidation occurring under anoxic conditions was discovered (Strous et al. 1999). Anammox (anaerobic ammonia oxidation) is carried out by prokaryotes belonging to the Planctomycetes phylum of Bacteria. The first described anammox bacterium was Brocadia anammoxidans. Anammox bacteria oxidize ammonia by using nitrite as the electron acceptor to produce gaseous nitrogen (Figure 6). Anammox bacteria were first discovered in anoxic bioreactors of wasterwater treatment plants but have since been found in a variety of aquatic systems, including low-oxygen zones of the ocean, coastal and estuarine sediments, mangroves, and freshwater lakes. In some areas of the ocean, the anammox process is considered to be responsible for a significant loss of nitrogen (Kuypers et al. 2005). However, Ward et al. (2009) argue that denitrification rather than anammox is responsible for most nitrogen loss in other areas. Whether anammox or denitrification is responsible for most nitrogen loss in the ocean, it is clear that anammox represents an important process in the global nitrogen cycle.


Denitrification

Denitrification is the process that converts nitrate to nitrogen gas, thus removing bioavailable nitrogen and returning it to the atmosphere. Dinitrogen gas (N2) is the ultimate end product of denitrification, but other intermediate gaseous forms of nitrogen exist (Figure 7). Some of these gases, such as nitrous oxide (N2O), are considered greenhouse gasses, reacting with ozone and contributing to air pollution.

Unlike nitrification, denitrification is an anaerobic process, occurring mostly in soils and sediments and anoxic zones in lakes and oceans. Similar to nitrogen fixation, denitrification is carried out by a diverse group of prokaryotes, and there is recent evidence that some eukaryotes are also capable of denitrification (Risgaard-Petersen et al. 2006). Some denitrifying bacteria include species in the genera Bacillus, Paracoccus, and Pseudomonas. Denitrifiers are chemoorganotrophs and thus must also be supplied with some form of organic carbon.

Denitrification is important in that it removes fixed nitrogen (i.e., nitrate) from the ecosystem and returns it to the atmosphere in a biologically inert form (N2). This is particularly important in agriculture where the loss of nitrates in fertilizer is detrimental and costly. However, denitrification in wastewater treatment plays a very beneficial role by removing unwanted nitrates from the wastewater effluent, thereby reducing the chances that the water discharged from the treatment plants will cause undesirable consequences (e.g., algal blooms).


Ammonification

When an organism excretes waste or dies, the nitrogen in its tissues is in the form of organic nitrogen (e.g. amino acids, DNA). Various fungi and prokaryotes then decompose the tissue and release inorganic nitrogen back into the ecosystem as ammonia in the process known as ammonification. The ammonia then becomes available for uptake by plants and other microorganisms for growth.


http://www.ck12.org/book/CK-12-Earth-Science-For-High-School/r2/section/18.2/

Nitrogen is also a very important element, used as a nutrient for plant and animal growth. First, the nitrogen must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them.

http://ellemedit1234.wordpress.com/2013/09/09/the-nitrogen-cycle/

The Nitrogen cycle is a lot more complex than the carbon cycle. Nitrogen is a very important element. It makes up almost 80% of our atmosphere, and it is an important component of proteins and DNA, both of which are the building blocks of animals and plants. Therefore without nitrogen we would lose one of the most important elements on this planet, along with oxygen, hydrogen and carbon. There are a number of stages to the nitrogen cycle, which involve breaking down and building up nitrogen and it’s various compounds.

There is no real starting point for the nitrogen cycle. It is an endless cycle. However we need a place to start from, and that is in the atmosphere. Nitrogen is very abundant in the atmosphere. Now through different processes nitrogen is constantly being removed from the atmosphere, and it is also being replaced again with more nitrogen. We are going to start with the process that removes nitrogen from the atmosphere, which is called nitrogen fixation. This is when nitrogen gas is transformed into various nitrogen compounds, such as ammonia, ammonium or even nitrate and nitrite. There are 3 ways in which the nitrogen gas can be fixed. The first method is slightly rare, but involves lightning. When lightning passes through the atmosphere it fixes the nitrogen, forming ammonia. However the other two processes are much more important when considering the nitrogen cycle. Both of the other methods are caused by bacteria.

One method involves free-living nitrogen-fixing bacteria. These bacteria convert the nitrogen into ammonia. These bacteria will naturally produce ammonia, however it will be used up in the production of amino acids. The other method involves mutualistic nitrogen-fixing bacteria, which live in the roots of different plants, including peas. They live in small bubbles, called nodules in the roots. This will provide the plants of the roots in which they live with amino acids.

1. http://www.astrobio.net/news-exclusive/nitrogen-ancient-rocks-sign-early-life/



Last edited by Admin on Sun Oct 22, 2017 5:32 am; edited 10 times in total

View user profile http://elshamah.heavenforum.com

Admin


Admin
http://ellemedit1234.wordpress.com/2013/09/09/the-nitrogen-cycle/

http://chemistry.about.com/od/geochemistry/ss/nitrogencycle.htm


http://belligerentdesign-asyncritus.blogspot.com.br/2010/01/cyanobacteria-evolutions-ignored.html

I am, and have long been, impressed with the great cycles in nature.
We see, inter alia, the carbon dioxide cycle, the oxygen cycle, the rain cycle and the nitrogen cycle.
Of these four, the nitrogen cycle has been of the greatest interest to me, because of its colossal importance to the survival of agriculture in all its forms.

We are faced with a tremendous problem, because nitrogen is one of the least reactive gases known, excepting only the rare gases of group 8 in the periodic table, such as helium. It just doesn't combine with anything under ordinary conditions.

The problem arises, of course, because nitrogen is an essential constituent of proteins and other substances, all needed for life to survive. No nitrogen: no proteins, no enzymes, no life. (By the way, when I say 'essential' I mean that survival is impossible without it.)

So how does nitrogen become available to living organisms? How could it?

The Almighty, as usual, has the answer that works perfectly.

Nitrogen becomes available in 3 ways:

1 Lightning discharges, at 30,000 deg C, force the combination of nitrogen and oxygen, to produce nitrogen dioxide, which dissolves in rain water to form nitric and nitrous acids, which then combine with compounds in the soil to produce nitrates and nitrites - which are utilisable by plants. So that's number one.

2 In the root nodules of leguminous plants, the bacterium Rhizobium leguminosarum has a symbiotic relationship with the plant. It 'fixes' atmospheric nitrogen, making it available to the plant, and in return, the plant provides the bacterium with salts etc for its survival. Curiously, haemoglobin is formed in the nodules too. It's role is not yet known with certainty, but researchers agree that it must have a function there.

Which, of course, drips another drop of poison into the evolutionist's already bitter cup: what on earth is haemoglobin doing in such a place? How does evolutionary biochemistry account for its existence? Well, easy. It can't. So nuts to evolutionary biochemistry.

3 By far, the greatest contribution to nitrogen fixation comes from the cyanobacteria. These bacteria have 'evolved (ho ho!)' the ability to take nitrogen from the air, [I wonder how they figured that little trick out???] convert it into their cellular material, and on dying, decompose and make nitrogen available to the soil. Without them, life would surely perish.

Just as an aside, it wasn't until 1918 that Haber received a nobel prize for inventing the process which took nitrogen from the air to make ammonia, using catalysts and very high temperatures. That's how difficult it is to do industrially. Yet, here were these little bacteria doing it for the last n billion years. At ambient temperature, give or take diurnal variation!!! So who deserves that Nobel Prize?

So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? The advanced nitrogen fixers hadn't 'evolved' yet.

So yet another evolutionary brick wall stares us in the face.

http://www.grisda.org/origins/60006.pdf

Zuill, H.A. and Standish, T.G., Irreducible interdependence: an ic-like ecological property potentially illustrated by the nitrogen cycle, Origins 60:6–40, 2007;

http://www.grisda.org/origins/60006.pdf

the cycle acts as a vital buffer to changes in nitrogen-containing molecules in the environment, while at the same time ensuring availability of reduced nitrogen for biological purposes.

http://creation.mobi/biblical-ecology

Nitrogen is crucial for the existence of all life and is a building block of amino acids needed for protein synthesis, as well as nucleotides and their nucleic acids. The nitrogen cycle’s function is to keep its various molecular forms in balance so that life can persist. Through five stages, atmospheric nitrogen is converted into nitrogen compounds that plants require and can assimilate, and it is then recycled back into the atmosphere again. Many chemical steps are involved in various parts of ecosystems and specific enzymes are needed at the right times and places. The nitrogen cycle is dependent on the carbon cycle and requires microbes and other creatures to work in concert. In turn, plants provide nutrition to animals. Amazingly, in order for certain chemical reactions to continue, plants contribute specific chemicals while the biomatrix provides what plants lack in order to complete the required chemical reactions. Many diverse genera are involved and this redundancy is important as a system back up should a certain taxon not be present.

Behe’s concept of irreducible complexity in biological systems41 was enlarged and extended to ecosystems, giving rise to a term ‘irreducible interdependence’.40 Behe discussed this concept in the context of biochemical reactions in single organisms. Zuill and Standish used the term ‘ecochemical pathways’ to refer to the series of biochemical reactions across multiple species, where each step of the reaction is mediated by one or several species. An irreducibly interdependent system has the following characteristics in this testable model:

Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone.
It must have a degree of specificity that in all probability could not have been produced by chance.
A given function or step in the system may be found in several different unrelated organisms.
The removal of any one of the individual biological steps will resort in the loss of function of the system.

The data suggest that the nitrogen cycle may be irreducibly interdependent based on the above criteria. No proposed neo-Darwinian mechanisms can explain the origin of such a system. Compounding matters, Zuill makes a strong case by suggesting that this biodiversity of multi-species interactions have always been required for biospheric regulation and had to have been built rapidly.42 Several of the above arguments are based on logical inferences, but many of these inferences can be further tested to determine if they meet interdependence criteria. This research could be extended to test other global cycles, and interaction between cycles, for irreducible interdependence.

View user profile http://elshamah.heavenforum.com

Admin


Admin
1. http://en.wikipedia.org/wiki/Nitrogen_fixation

Nitrogen fixation is a process by which nitrogen (N2) in the atmosphere is converted into ammonia (NH3).[1] Atmospheric nitrogen or molecular nitrogen (N2) is relatively inert: it does not easily react with other chemicals to form new compounds. The fixation process frees up the nitrogen atoms from their diatomic form (N2) to be used in other ways.

Nitrogen fixation, natural and synthetic, is essential for all forms of life because nitrogen is required to biosynthesize basic building blocks of plants, animals and other life forms, e.g., nucleotides for DNA and RNA and amino acids for proteins.



http://www.answersingenesis.org/articles/am/v7/n3/forest-amid-trees

ots of different kinds of creatures must work in sync for ecosystems to survive. Consider the nitrogen cycle.

Nitrogen is a basic element in all living things. Yet the chemical bonds of nitrogen gas are so strong that it is not usable until it is “fixed” into a form plants can use. Researchers have identified five major stages, each requiring different organisms with specialized proteins.

Biological Nitrogen Fixation. Nitrogen gas (N2) must first be changed into ammonia (NH3). A diversity of bacteria have the proteins necessary to do this. If one bacterial species is not present, another one can pick up the slack. This redundancy, or backup system, is marvelously designed.

Since oxygen hinders this chemical process, fixation needs to take place in an oxygen-less chamber. Plants provide bacteria with little chambers (nodules) in their roots.

A special protein (leghaemoglobin) then carries oxygen away so it will not interfere. Amazingly, the plant and bacteria cooperatively manufacture different parts of this protein. After the plant has fixed enough nitrogen, it communicates to the bacteria and they both stop production.

Nitrification. Ammonia needs to be changed into nitrite (NO2–) and then nitrate (NO3–). This requires a different suite of bacteria and some fungi. In some cases, bacteria can only change ammonia into nitrite, so they “hand it off” to other bacteria to finish the job. This form of nitrogen readily dissolves in water to be transported and used by organisms far away.

Denitrification. A different group of microbes change nitrate back into nitrogen gas (N2) or nitrous oxide (N2O). Without this process, nitrates could accumulate in water or soil, seriously harming the health of the ecosystem.

Assimilation. Nitrates were made in step 2 because plants can easily absorb that chemical. Later it must be changed back to ammonia to make other compounds needed for life, such as amino acids.

Excretion and Decay. A huge clean-up crew of diverse organisms breaks down waste products and recycles the nitrogen.

Just like a factory assembly line, all the workers must be in the right places, at the right time, with the right tools to make the product.1 Systems like the nitrogen cycle appear to be irreducibly complex. For them to work, all the components had to be in place at the same time—amazing evidence of a loving, all-wise Creator who made the components in just six days.

1H. A. Zuill and T. G. Standish, “Irreducible Interdependence: An IC-like Ecological Property Potentially Illustrated by the Nitrogen Cycle,” Origins 60 (2007): 6–40.

Whilst the chemical abundance is uncertain it is ridiculous to think that the spontaneous formation of say amino acids could not happen outside the lab some 4 billion years ago. Without cyanobacteria - no fixed nitrogen is available.

Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised.

Without DNA, no amino-acids,protein, or cyanobacteria are possible.

There are several other points here, in addition.

These bacteria also photosynthesise (a process requiring a large number of proteins, both in the execution of the reactions, and in the structure of the membranes of the chloroplasts). Let's say 30 for argument's sake.

They fix nitrogen - and so require that marvellous enzyme nitrogenase, which is really a combination of 2 separate enzymes, proteins to be precise.

None of these, as shown above, can be made without fixed nitrogen.

Nitrogen cannot be fixed without them. So which came first, the chicken or the egg//http://en.wikipedia.org/wiki/Amino_acid_synthesis

A fundamental problem for biological systems is to obtain nitrogen in an easily usable form. This problem is solved by certain microorganisms capable of reducing the inert N≡N molecule (nitrogen gas) to two molecules of ammonia in one of the most remarkable reactions in biochemistry. Ammonia is the source of nitrogen for all the amino acids.

To obtain nitrogen in usable form, you need nitrogen fixation :

http://en.wikipedia.org/wiki/Nitrogen_fixation

Nitrogen fixation, natural and synthetic, is essential for all forms of life because nitrogen is required to biosynthesize basic building blocks of plants, animals and other life forms, e.g., nucleotides for DNA and RNA and amino acids for proteins.

How can this occur :

1) Nitrogen fixation occurs naturally in the air by means of lightning. It forces the combination of nitrogen and oxygen, to produce nitrogen dioxide, which dissolves in rain water to form nitric and nitrous acids, which then combine with compounds in the soil to produce nitrates and nitrites - which are utilisable by plants

the causes of lightning are still not fully understood .

2)Free-Living Heterotrophs
Many heterotrophic bacteria live in the soil and fix significant levels of nitrogen without the direct interaction with other organisms. Examples of this type of nitrogen-fixing bacteria include species of Azotobacter, Bacillus, Clostridium, and Klebsiella.

Associative Nitrogen Fixation
Species of Azospirillum ( bacteria )are able to form close associations with several members of the Poaceae (grasses), including agronomically important cereal crops, such as rice, wheat, corn, oats, and barley.

Nitrogen Fixation
Many microorganisms fix nitrogen symbiotically by partnering with a host plant.

Legume Nodule Formation
The Rhizobium or Bradyrhizobium bacteria colonize the host plant’s root system and cause the roots to form nodules to house the bacteria

By far, the greatest contribution to nitrogen fixation comes from the cyanobacteria.

These bacteria have the ability to take nitrogen from the air, [I wonder how they figured that little trick out???] convert it into their cellular material, and on dying, decompose and make nitrogen available to the soil.

So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? The advanced nitrogen fixers hadn't 'evolved' yet.

http://www.nature.com/.../an-evolutionary-perspective-on...

The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. However, to be metabolically useful, atmospheric nitrogen must be reduced. This process, known as nitrogen fixation, occurs only in certain types of bacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N≡N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation).

http://mbe.oxfordjournals.org/content/21/3/541.long

Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective.

http://chemwiki.ucdavis.edu/.../Nitrogenase/Nitrogenase_1

Nitrogenase is a unique enzyme with a crucial function that is distinct to bacteria that utilize it, has unique structure and symmetry, and is sensitive to other compounds that inhibits its functioning. It is “an enzymatic complex which enables fixation of atmospheric nitrogen” . The unique structure of nitrogenase is almost completely known because of the extensive research that has been done on this enzyme. Nitrogenase can also bind to compounds other than nitrogen gas, which can inhibit and decrease its production of ammonia to the rest of the organism’s body. Without proper functioning, the bacteria that utilize nitrogenase would not be able to survive, and other organisms that depend on these bacteria would also die.

Nitrogenase is unique in its ability to fix nitrogen, so that it is more reactive and able to be applied in other reactions that help organisms grow and thrive. David Goodsell states, “Nitrogen is needed by all living things to build proteins and nucleic acids” [4]. However, nitrogen gas, N2, is an inert gas that is stabilized by its triple bond [5], and is difficult for living organisms to use as a source of nitrogen because the molecule’s stability. Nitrogenase is used to separate nitrogen gas, N2, and transforms it into ammonia, NH3 in the reaction:

N2 + 8H+ + 8e- + 16 ATP + 16H2O ----> 2NH3 + H2 + 16ADP + 16Pi

In the form of ammonia organisms have a useable source of nitrogen that is more reactive and can be used to create proteins and nucleic acids that are also necessary for the organism. According to the Peters and Szilagyi, “Three types of nitrogenase are known, called molybdenum (Mo) nitrogenase, vanadium (V) nitrogenase and iron-only (Fe) nitrogenase” and the molybdenum nitrogenase,crystal structure shown in Figure 2, is the one that has been studied the most of the three . The nitrogenase enzyme breaks up a diatomic nitrogen gas molecule using a large number of ATP and 8 electrons to create two ammonia molecules and hydrogen gas for each molecule of nitrogen gas . As a result, the bacteria that utilize this enzyme must expend much of their energy, in the form of ATP, so that they will constantly obtain a steady source of nitrogen. Without nitrogenase’s function of fixing nitrogen gas into ammonia, then organisms would not be able to thrive since they would not receive a source of nitrogen for other important reactions.

How could those regulatory machines evolve at precisely the right rate so as to drop into the right place at precisely the right time to effect proper assembly of the nitrogenase machinery?

Fine, L.W., Chemistry Decoded, Oxford University Press, London, pp. 320-330, 1976.

“Nature is really good at it (nitrogen-splitting), so good in fact that we’ve had difficulty in copying chemically the essence of what bacteria do so well”

http://en.wikipedia.org/wiki/Nitrogen_cycle

The plant provides amino acids to the bacteroids so ammonia assimilation is not required and the bacteroids pass amino acids (with the newly fixed nitrogen) back to the plant, thus forming an interdependent relationship

So there we have a classic chicken and egg problem........


Nitrogen becomes available in 4 ways:

1 Lightning discharges, at 30,000 deg C, force the combination of nitrogen and oxygen, to produce nitrogen dioxide, which dissolves in rain water to form nitric and nitrous acids, which then combine with compounds in the soil to produce nitrates and nitrites - which are utilisable by plants. So that's number one. Lightening can break the bond but they do not produce sufficient quantities of the biologically reactive nitrogen to be of any substantial use.

2 In the root nodules of leguminous plants, the bacterium Rhizobium leguminosarum has a symbiotic relationship with the plant. It 'fixes' atmospheric nitrogen, making it available to the plant, and in return, the plant provides the bacterium with salts etc for its survival. Curiously, haemoglobin is formed in the nodules too. It's role is not yet known with certainty, but researchers agree that it must have a function there.

Which, of course, drips another drop of poison into the evolutionist's already bitter cup: what on earth is haemoglobin doing in such a place? How does evolutionary biochemistry account for its existence? Well, easy. It can't. So nuts to evolutionary biochemistry.

3.the release of these compounds during organic matter decomposition

4. By far, the greatest contribution to nitrogen fixation comes from the cyanobacteria. These bacteria have 'evolved (ho ho!)' the ability to take nitrogen from the air, [I wonder how they figured that little trick out???] convert it into their cellular material, and on dying, decompose and make nitrogen available to the soil. Without them, life would surely perish.






So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? The advanced nitrogen fixers hadn't 'evolved' yet.

Through five stages, atmospheric nitrogen is converted into nitrogen compounds that plants require and can assimilate, and it is then recycled back into the atmosphere again.

The nitrogenase enzyme breaks up a diatomic nitrogen gas molecule using a large number of ATP and 8 electrons to create two ammonia molecules and hydrogen gas for each molecule of nitrogen gas . As a result, the bacteria that utilize this enzyme must expend much of their energy, in the form of ATP, so that they will constantly obtain a steady source of nitrogen. Without nitrogenase’s function of fixing nitrogen gas into ammonia, then organisms would not be able to thrive since they would not receive a source of nitrogen for other important reactions.

How could those regulatory machines evolve at precisely the right rate so as to drop into the right place at precisely the right time to effect proper assembly of the nitrogenase machinery?


http://creation.mobi/biblical-ecology

The nitrogen cycle is dependent on the carbon cycle and requires microbes and other creatures to work in concert.

An irreducibly interdependent system has the following characteristics in this testable model:

Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone.
It must have a degree of specificity that in all probability could not have been produced by chance.
A given function or step in the system may be found in several different unrelated organisms.
The removal of any one of the individual biological steps will resort in the loss of function of the system.


Microbes are also a crucial component in biogeochemical cycling. These cycles consist of the paths elements take through the global system for proper functioning and persistence of life. If microbes did not exist, the critical carbon, nitrogen and phosphorous cycles would not be possible and life would cease. Life affects chemistry and chemistry affects life.

http://rstb.royalsocietypublishing.org/content/363/1504/2731.long

The atmosphere has apparently been oxygenated since the ‘Great Oxidation Event’ ca 2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in ca 2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as ca 2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at ca 3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U–Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.

Nitrogen fixation in methanogens: the archaeal perspective.

http://www.ncbi.nlm.nih.gov/pubmed/11471757

http://www.horizonpress.com/cimb/v/v2/v2n404.pdf

The methanogenic Archaea bring a broadened perspective to the field of nitrogen fixation. Biochemical and genetic studies show that nitrogen fixation in Archaea is evolutionarily related to nitrogen fixation in Bacteria and operates by the same fundamental mechanism. How ?? At least six nif genes present in Bacteria (nif H, D, K, E, N and X) are also found in the diazotrophic methanogens. So what ?? Most nitrogenases in methanogens are probably of the molybdenum type. However, differences exist in gene organization and regulation. All six known nif genes of methanogens, plus two homologues of the bacterial nitrogen sensor-regulator glnB, occur in a single operon in Methanococcus maripaludis. nif gene transcription in methanogens is regulated by what appears to be a classical prokaryotic repression mechanism. At least one aspect of regulation, post-transcriptional ammonia switch-off, involves novel members of the glnB family. Phylogenetic analysis suggests that nitrogen fixation may have originated in a common ancestor of the Bacteria and the Archaea.

A separate analysis by parsimony gave essentially the same results as the distance matrix analysis. nifD and nifE
are evidently paralogous, that is, related via an ancient gene duplication. Consequently, nifD genes provide a root for the nifE tree and vice versa.

View user profile http://elshamah.heavenforum.com

Admin


Admin
Amino Acids and Nucleotide are part of the Nitrogen Cycle

Nitrogen and sulfur are important constituents of biological macromolecules. Nitrogen and sulfur atoms pass from compound to compound and between organisms and their environment in a series of reversible cycles. Although molecular nitrogen is abundant in the Earth's atmosphere, nitrogen is chemically unreactive as a gas. Only a few living species are able to incorporate it into organic molecules, a process called nitrogen fixation. Nitrogen fixation occurs in certain microorganisms and by some geophysical processes, such as lightning discharge. It is essential to the biosphere as a whole, for without it life could not exist on this planet. Only a small fraction of the nitrogenous compounds in today's organisms, however, is due to fresh products of nitrogen fixation from the atmosphere. Most organic nitrogen has been in circulation for some time, passing from one living organism to another. Thus present-day nitrogen-fixing reactions can be said to perform a "topping-up" function for the total nitrogen supply. Vertebrates receive virtually all of their nitrogen from their dietary intake of proteins and nucleic acids. In the body these macromolecules are broken down to amino acids and the components of nucleotides, and the nitrogen they contain is used to produce new proteins and nucleic acids-or utilized to make other molecules. About half of the 20 amino acids found in proteins are essential amino acids for vertebrates (Figure 2-87), which means that they cannot be synthesized from other ingredients of the diet. The others can be so synthesized, using a variety of raw materials, including intermediates of the citric acid cycle as described previously. The essential amino acids are made by plants and other organisms, usually by long and energetically expensive pathways that have been lost in the course of vertebrate evolution. Roshanl(eab 02l-66950639 The nucleotides needed to make RNA and DNA can be synthesized using specialized biosynthetic pathways. All of the nitrogens in the purine and pyrimidine bases (as well as some of the carbons) are derived from the plentiful amino acids glutamine, aspartic acid, and glycine, whereas the ribose and deoxyribose sugars are derived from glucose. There are no "essential nucleotides" that must be provided in the diet. Amino acids not used in biosynthesis can be oxidized to generate metabolic energy. Most of their carbon and hydrogen atoms eventually form COz or HzO, whereas their nitrogen atoms are shuttled through various forms and eventually appear as urea, which is excreted. Each amino acid is processed differently, and a whole constellation of enzymatic reactions exists for their catabolism. 

 Sulfur is abundant on Earth in its most oxidized form, sulfate (SOaz-)T. o convert it to forms useful for life, sulfate must be reduced to sulfide (S2-), the oxidation state of sulfur required for the synthesis of essential biological molecules. These molecules include the amino acids methionine and cysteine, coenzyme A (see Figure 2-62), and the iron-sulfur centers essential for electron transport (see Figure 14-23). The process begins in bacteria, fungi, and plants, where a special group of enzymes use ATP and reducing power to create a sulfate assimilation pathway. Humans and other animals cannot reduce sulfate and must therefore acquire the sulfur they need for their metabolism in the food that they eat.

View user profile http://elshamah.heavenforum.com

Admin


Admin
When we think about the elements that are essential for life on Earth, we hardly ever consider molybdenum. The biological role of molybdenum can only be appreciated when put in perspective. Nitrogen is the fourth most abundant element in living organisms (only behind hydrogen, oxygen and carbon) and life on Earth depends on the nitrogen biogeochemical cycle to keep this element in forms that can be used by the organisms. Noteworthy, the “closing” of the nitrogen cycle, with the atmospheric dinitrogen fixation into ammoniu–(Figure 1.1, blue arrow), depends virtually entirely on the trace element molybdenum :



nitrogenase, a prokaryotic enzyme responsible for dinitrogen reduction to ammonium, requires one molybdenum atom in its active site† (Figure 1.3b; see Section 1.4.5 and ref.
55).



The few organisms possessing this enzyme are capable of producing their own reduced (“fixed”) nitrogen forms, using directly the atmospheric dinitrogen, the largest nitrogen source (biological nitrogen fixation is the main route by which nitrogen enters the biosphere). All other organisms, the vast majority of life on Earth, depend on the availability of ammonium and nitrate (from soils, oceans and other organisms).

With this wide perspective in mind, the molybdenum biological role certainly assumes another dimension. In fact, it was recently proposed that the lack of molybdenum, while hampering the existence of an efficient nitrogenase, could have been the limiting factor for life evolution and expansion on early Earth. However, the involvement of molybdenum in the nitrogen cycle is not restricted to the dinitrogen fixation, as the element is also essential for the reduction of nitrate to nitrite and for the oxidation of nitrite to nitrate (Figure 1.1, grey arrows), both processes being exclusively dependent (as far as is presently known) on the molybdenum- containing enzymes nitrate reductases (from both prokaryotic and eukaryotic sources) and nitrite oxidoreductases (from prokaryotes only). Noteworthy, molybdenum has also been suggested to be essential for nitrite reduction to nitric oxide for biological signalling purposes. Nitric oxide is a signalling molecule involved in several physiological processes, in both prokaryotes and eukaryotes, and nitrite is presently recognized as a nitric oxide source particularly relevant to cell signalling and survival under challenging conditions. Nitrite-dependent signalling pathways have been described in mammals, plants and also bacteria, and are carried out by proteins present in cells to carry out other functions, including several molybdoenzymes (which thus form a new class of “non-dedicated” nitric oxide-forming nitrite reductases): mammalian xanthine oxidoreductase, aldehyde oxidase, sulfite oxidase and mitochondrial amidoxime reducing component, plant nitrate reductase and bacterial aldehyde oxidoreductase and nitrate reductases. Molybdenum is also involved in the carbon cycle. The first example that comes to mind is provided by the formate dehydrogenases that are used by acetogens to fix carbon dioxide (reduce it) into formate and eventually form acetate; but molybdenum is also present in carbon monoxide dehydrogenases (catalyzing the oxidation of carbon monoxide to carbon dioxide), aldehyde oxidoreductases (catalyzing the interconversion between aldehydes and carboxylic acids) and in other formate dehydrogenases (that are involved in physiological pathways where formate is oxidized to carbon dioxide). The primitive carbon cycle would have also been dependent on molybdenum, as the metal (together with tungsten) would have been essential for the earliest, strictly anaerobic, organisms to handle aldehydes and carboxylic acids, catalyzing their interconversion

Molybdenum also plays several other “carbon-related” roles in modern higher organisms. The aldehyde oxidase of higher plants is responsible for the oxidation of abscisic aldehyde to abscisic acid (a plant hormone involved in development processes and in a variety of abiotic and biotic stress responses) and has been implicated in the biosynthesis of indole-3-acetic acid (an auxin phytohormone). The mammalian aldehyde oxidases have been suggested to participate in the formation of retinoic acid (a metabolite of retinol (vitamin A) that is involved in growth and development) and in the metabolism of xenobiotic compounds, where they would catalyze the hydroxylation of carbon centres of heterocyclic aromatic compounds and the oxidation of aldehydic groups The dependence of higher plants and animals on molybdenum is also observed in purine catabolism, where xanthine oxidoreductase is involved in the hydroxylation of hypoxanthine and xanthine into urate. Noteworthy, involvement of molybdenum in purine metabolism is common to virtually all forms of life and only a small number of organisms use other mechanisms to oxidize xanthine (e.g. some yeasts), thus confirming the essential role of molybdenum for life on Earth. Another important aspect of molybdenum in biology can be seen in sulfite- oxidizing enzymes, which are used by almost all forms of life in the catabolism of sulfur-containing amino acids and other sulfur-containing compounds, oxidizing sulfite to sulfate. Certainly, sulfite oxidase is one of the most striking examples of the human dependence on molybdenum. Sulfite (derived not only from the catabolism of sulfur-containing amino acids, but also from sulfur-containing xenobiotic compounds) is toxic and its controlled oxidation to sulfate is critical for survival. Underscoring this vital role, human sulfite oxidase deficiency results in severe neonatal neurological problems, including attenuated growth of the brain, mental retardation, seizures and early death.‡ Molybdenum-dependent sulfite-oxidizing enzymes are also important for some prokaryotes that are able to generate energy from the respiratory oxidation of inorganic sulfur compounds – hence, extending the role of molybdenum to the sulfur cycle.

Why do living organisms expend so much effort to use these metals in a (comparatively) small number of reactions? This effort (including synthesizing the protein machinery to scavenge the metals from the environment, producing and inserting the specialized cofactors and regulating the whole process) underscores how important both metals would have been, and still are to extant organisms, particularly in the case of molybdenum.

View user profile http://elshamah.heavenforum.com

Sponsored content


View previous topic View next topic Back to top  Message [Page 1 of 1]

Permissions in this forum:
You cannot reply to topics in this forum