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Theory of Intelligent Design, the best explanation of Origins » Molecular biology of the cell » Metabolism » How biosynthesis of amino acids points to a created process

How biosynthesis of amino acids points to a created process

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How  biosynthesis of amino acids points to a created process

http://reasonandscience.heavenforum.org/t1397-how-biosynthesis-of-amino-acids-points-to-a-created-process

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.


Amino acids are the building blocks that make up proteins. Twenty chemically distinct amino acids comprise the proteins found in every organism on Earth. That is, the set of amino acids used in biology is universal. Yet, hundreds of amino acids exist in nature. Why does nature use the specific set of 20 amino acids, and not  others existing, to make  proteins ?  1

This question leads to other related why questions:

- Why are proteins built from amino acids? Why not build them from the chemically simpler hydroxy acids?
- Why do only amino acids and sugars  only in one enantiomeric form in most biological systems exist on earth ?
- Why are the amino acids in proteins α-amino acids? Why not β- or γ- or δ-amino acids?
- Why do all the amino acids in proteins have an α-hydrogen?
- Why are there no N-alkyl amino acids in proteins?

Many naturally occurring amino acids possess these structural features. Shouldn’t at least some of these alternative compounds have made their way into proteins? Why did they not ? The team conducted a quantitative comparison of the range of chemical and physical properties possessed by the 20 protein-building amino acids versus random sets of amino acids that could have been selected from early Earth’s hypothetical prebiotic soup. They concluded that the set of 20 amino acids is optimal.

It turns out that the set of amino acids found in biological systems possess properties that evenly and uniformly varies across a broad range of sizes, charges, and hydrophobicities. They also demonstrate that the amino acids selected for proteins is a “highly unusual set of 20 amino acids; a maximum of 0.03% random sets out-performed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously.” 2

The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. 3  There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment.

Polymer formation in aqueous environments would most likely have been necessary on early Earth because the liquid ocean would have been the reservoir of amino acid precursors needed for protein synthesis. 3 

A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10-338 molar, we would need an ocean with a volume equal to 10229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.

 Sidney Fox, an amino acid chemist, and one of my professors in graduate school, recognized the problem and set about constructing an alternative. Since water is unfavorable to peptide bond formation, the absence of water must favor the reaction. Fox attempted to melt pure crystalline amino acids in order to promote peptide bond formation by driving off water from the mix. He discovered to his dismay that most amino acids broke down to a tarry degradation product long before they melted. After many tries he discovered two of the 20 amino acids, aspartic and glutamic acid, would melt to a liquid at about 200oC. He further discovered that if he were to dissolve the other amino acids in the molten aspartic and glutamic acids, he could produce a melt containing up to 50% of the remaining 18 amino acids. It was no surprise then that the amber liquid, after cooking for a few hours , contained polymers of amino acids with some of the properties of proteins. He subsequently named the product proteinoids. The polymerized material can be poured into an aqueous solution, resulting in the formation of spherules of protein-like material which Fox has likened to cells. Fox has claimed nearly every conceivable property for his product, including that he had bridged the macromolecule to cell transition. He even went so far as to demonstrate a piece of lava rock could substitute for the test tube in proteinoid synthesis and claimed the process took place on the primitive earth on the flanks of volcanoes. 

Experimental evidence indicates that if there are bonding preferences between amino acids, they are not the ones found in natural organisms. There are three basic requirements for a biologically functional protein. 4

One: It must have a specific sequence of amino acids. At best prebiotic experiments have produced only random polymers. And many of the amino acids included are not found in living organisms.

Second: An amino acid with a given chemical formula may in its structure be either “righthanded” (D-amino acids) or “left-handed” (L-amino acids). Living organisms incorporate only L-amino acids. However, in prebiotic experiments where amino acids are formed approximately equal numbers of D- and L-amino acids are found. This is an “intractable problem” for chemical evolution (p. vi).

Third: In some amino acids there are more positions than one on the molecule where the amino and carboxyl groups may join to form a peptide bond. In natural proteins only alpha peptide bonds (designating the location of the bond) are found. In proteinoids, however, beta, gamma and epsilon peptide bonds largely predominate. Just the opposite of what one would expect if bonding preferences played a role in prebiotic evolution.



What Is an Amino Acid Made Of?

As implied by the root of the word (amine), the key atom in amino acid composition is nitrogen. 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). 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. All organisms contain the enzymes glutamate dehydrogenase and glutamine synthetase, which convert ammonia to glutamate and glutamine, respectively. Amino and amide groups from these two compounds can then be transferred to other carbon backbones by transamination and transamidation reactions to make amino acids. Interestingly, glutamine is the universal donor of amine groups for the formation of many other amino acids as well as many biosynthetic products. Glutamine is also a key metabolite for ammonia storage. All amino acids, with the exception of proline, have a primary amino group (NH2) and a carboxylic acid (COOH) group. They are distinguished from one another primarily by , appendages to the central carbon atom.


The key atom in amino acid composition is nitrogen.

Nitrogen must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them. Nitrogenase is the only family of enzymes capable of breaking this bond


Another tiny but marvellous bit of biochemistry which could be nominated to such a position is a mechanism which might be termed ‘the molecular sledgehammer’.

To appreciate the work done by this ‘sledgehammer’, it is important to understand the role of the element nitrogen in the living world. The two main constituents of our atmosphere, oxygen (21%) and nitrogen (78%), both play important roles in the makeup of living things. Both are integral parts of the [b]amino acids which join together in long chains to make all proteins, and of the nucleotides which do the same thing to form DNA and RNA. Getting elemental oxygen (O2) to split apart into atoms and take part in the reactions and structures of life is not hard; in fact, oxygen is so reactive that keeping it from getting into where it's not wanted becomes the more challenging job. However, elemental nitrogen poses the opposite problem. Like oxygen, it is diatomic (each molecule contains two N atoms) in its pure form (N2); but, unlike oxygen, each of its atoms is triple-bonded to the other. 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?

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Nitrogen splitting


The searching chemists of a century ago did not realize that an ingenious method for cracking nitrogen molecules was already in operation. This process did not require high temperatures or pressures, and was already working efficiently and quietly to supply the Earth's topsoil with an estimated 100 million tons of nitrogen every year. This process’ inventor was not awarded a Nobel Prize, nor was it acclaimed with much fanfare as the work of genius that it is.[b] This process is humbly carried on by a few species of the ‘lowest’ forms of life on Earth—bacteria and blue-green algae (Cyanobacteria).

Some of these tiny yet amazingly sophisticated organisms live in symbiosis (mutually beneficial ‘living together’) with certain ‘higher’ plants, known as legumes. The leguminous plants include peas, soybeans and alfalfa, long valued as crops because of their unique ability to enrich the soil. The microbes invade their roots, forming visible nodules in which the process of nitrogen cracking is carried on.

Modern biochemistry has given us a glimpse of the enzyme system used in this process. The chief enzyme is nitrogenase, which, like hemoglobin, is a large metalloprotein complex.2 Like Fritz Haber’s process, and like catalytic converters in cars today, it uses the principle of metal catalysis. However, like all biological enzymatic processes, it works in a more exact and efficient way than the clumsy chemical processes of human invention. Several atoms of iron and molybdenum are held in an organic lattice to form the active chemical site. 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.

One author summed up the situation well by remarking, ‘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.’4 If one merely substitutes the name of God for the word 'nature', the real picture emerges.

Creationists  are often accused of having the same easy answer for any question about specific origin of things in nature: the 'God of the gaps' did it. But this criticism can be easily turned around. What answers do propnents of natural mechanisms  give to explain the origin of microscopic marvels like the molecular sledgehammer? They can't explain them scientifically, so they resort to a standard liturgy, worshipping the power of blind chance and natural selection.
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Amino acids are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid

Amines are organic compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group.

A  Carboxylic acid is an organic compound that contains a carboxyl group (C(O)OH).[1] The general formula of a carboxylic acid is R−C(O)OH with R referring to the rest of the (possibly quite large) molecule. Carboxylic acids occur widely and include the amino acids and acetic acid (as vinegar).

Amino Acid:

1. These are composed of one carboxyl group and one or more amino groups.

2. There are twenty two different types of amino acids.

3. Some important amino acids are glycine, alanine, serine, valine, etc.

4. Amino acids are building blocks of all proteins.

5. Amino acids are linked by peptide bonds to form protein or are present freely in the protoplasm.

Nucleic Acid:

1. These are composed of pentose sugar,nitrogenous base and phosphate group.

2. There are two types of nucleic acids.

3. The two types of nucleic acids are DNA and RNA.

4. DNA is the genetic material. RNA is mainly responsible for protein synthesis and is genetic material in some viruses.

5. DNA is associated with histone protein in chromosome in eukaryotic cell or is present in naked condition in prokaryotes, mitochondria and plastids. RNA is also present in free state.

Amino acids  are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues.

They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins.


Proteinogenic_amino_acid


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

Amine

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

Amines are organic compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group.

Carboxylic_acid

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

A carboxylic acid  is an organic acid characterized by the presence of at least one carboxyl group.The general formula of a carboxylic acid is R-COOH, where R is some monovalent functional group.

Carbonyl

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

In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups.

Amino_acid_synthesis

http://www.tamu.edu/faculty/bmiles/lectures/biosynaa.pdf

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

Amino acid synthesis is the set of biochemical processes (metabolic pathways) by which the various amino acids are produced from other compounds. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesise all amino acids. For example, humans are able to synthesise only 12 of the 20 standard amino acids.

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. The carbon backbonescome from the glycolytic pathway, the pentose phosphate pathway, or the citric acid cycle.

http://www.tamu.edu/faculty/bmiles/lectures/biosynaa.pdf

The carbon skeletons come from intermediates of glycolysis, the pentose phosphate pathway and the citric acid cycle.

Glycolysis

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

Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

Glycolysis is a determined sequence of ten enzyme-catalyzed reactions.
The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat.

Glycolysis occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic pathways. It occurs in the cytosol of the cell.

https://releasingthetruth.wordpress.com/page/2/

Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).Yeast cells obtain energy under anaerobic conditions using a very similar process called alcoholic fermentation,  also referred to as ethanol fermentation, is a biological process in which sugars such as glucose, fructose, and sucrose are converted into cellular energy and thereby produce ethanol and carbon dioxide as metabolic waste products.

Glycolysis requires 11 enzymes which degrade glucose to lactic acid (Fig. 2). Alcoholic fermentation follows the same enzymatic pathway for the first 10 steps. The last enzyme of glycolysis, lactate dehydrogenase, is replaced by two enzymes in alcoholic fermentation. These two enzymes, pyruvate decarboxylase and alcoholic dehydrogenase, convert pyruvic acid into carbon dioxide and ethanol in alcoholic fermentation.

The most commonly accepted evolutionary scenario states that organisms first arose in an atmosphere lacking oxygen.1,2 Anaerobic fermentation is supposed to have evolved first and is considered the most ancient pathway for obtaining energy. However, there are several scientific odds against that.

First of all, it takes ATP energy to start the process that will only later generate a net gain in ATP. Two ATPs are put into the glycolytic pathway for priming the reactions, the expenditure of energy by conversion of ATP to ADP being required in the first and third steps of the pathway (Fig. 2). A total of four ATPs are obtained only later in the sequence, making a net gain of two ATPs for each molecule of glucose degraded. The net gain of two ATPs is not realized until the tenth enzyme in the series catalyzes phosphoenolpyruvate to ATP and pyruvic acid (pyruvate). This means that neither glycolysis nor alcoholic fermentation realizes any gain in energy (ATP) until the tenth enzymatic breakdown.

Enzymes are proteins consisting of amino acids united in polypeptide chains. Their complexity may be illustrated by the enzyme glyceraldehyde 3-phosphate dehydrogenase, which is the enzyme that catalyzes the oxidation of phosphoglyceraldehyde in glycolysis and alcoholic fermentation. Glyceraldehyde phosphate dehydrogenase consists of four identical chains, each having 330 amino acid residues. The possible number of different combinations of these amino acid chains is infinite.

To illustrate, let us consider a simple protein containing only 100 aim acids. There are 20 different kinds of L-amino acids in proteins, and each can be used repeatedly in chains of 100. Therefore, they could be arranged in 20^100 or 10^130 different ways. Even if a hundred million billion of these (10^17) combinations could function for a given purpose, there is only one chance in 10^113 of getting one of these required amino acid sequences in a small protein consisting of 100 amino acids. By comparison, Sir Arthur Eddington has estimated there are no more than 10^80 (or 3,145 x 10^79) particles in the universe! Consider the 10 enzymes of the glycolytic pathway. If each of these were a small protein having 100 amino acid residues with some flexibility and a probability of 1 in 10^113 or 10^-113, the probability for arranging the amino acids for the 10 enzymes would be: P = 10^-1,130 or 1 in 10^1,130, and this result is only the odds against producing the 10 glycoytic enzymes by chance. It is estimated that the human body contains 25,000 enzymes. If each of these were only a small enzyme consisting of 100 amino acids with a probability of 1 in 10^-113, the probability of getting all 25,000 would be (10^-113)^25,000, which is 1 chance in 10^2,825,000…

There are still other problems with that theory. There are numerous complex regulatory mechanisms which control these chemical pathways. For example, phosphofructokinase is a regulatory enzyme which limits the rate of glycolysis. Glycogen phosphorylase is also a regulatory enzyme; it converts glycogen to glucose-1-phosphate and thus makes glycogen available for glycolytic breakdown. In complex organisms there are several hormones such as somatotropin, insulin, glucagon, glucocorticoids, adrenaline thyroxin and a host of others which control utilization of glucose.

In addition, complex cofactors are absolutely essential for glycolysis. One of the two key ATP energy harvesting steps in glycolysis requires a dehydrogenase enzyme acting in concert with the “hydrogen shuttle” redox reactant, nicotinamide adenine dinucleotide (NAD+). To keep the reaction sequence going, the reduced cofactor (NADH + H +) must be continuously regenerated by steps later in the sequence (Fig. 2), which requires one enzyme in glycolysis (lactic dehydrogenase) and another (alcohol dehydrogenase) in alcoholic fermentation.

Further, at one point, an intermediate in the glycolytic pathway is “stuck” with a phosphate group (needed to make ATP) in the low energy third carbon position. A remarkable enzyme, a “mutase” (Step Cool, shifts the phosphate group to the second carbon position—but only in the presence of pre-existent primer amounts of an extraordinary molecule, 2,3-diphosphoglyceric acid. Actually, the shift of the phosphate from the third to the second position using the “mutase” and these “primer” molecules accomplishes nothing notable directly, but it “sets up” the ATP energy-harvesting reaction which occurs two steps later!

Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways

http://darwins-god.blogspot.com.br/2011/07/glycolysis-and-citric-acid-cycle.html

Automobiles have incredible engines, cooling systems, drive trains, and so forth, but all of this must be controlled. The accelerator, gears and brakes are essential in automobile design. This is even more true in biology where regulation and control at all levels is crucial and incredibly complex, particularly since so much of the control is performed automatically. At the cellular level, the cell’s machines—the proteins—are controlled at several levels. As one leading textbook describes:

   A living cell contains thousands of enzymes, many of which operate at the same time and in the same small volume of the cytosol. By their catalytic action, these enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs.

   Regulation occurs at many levels. At one level, the cell controls how many molecules of each enzyme it makes by regulating the expression of the gene that encodes that enzyme. The cell also controls enzymatic activities by confining sets of enzymes to particular subcellular compartments, enclosed by distinct membranes. The rate of protein destruction by targeted proteolysis represents yet another important regulatory mechanism. But the most rapid and general process that adjusts reaction rates operates through a direct, reversible change in the activity of an enzyme in response to specific molecules that it encounters.

So the cell controls its proteins by controlling how many it creates and destroys, and by confining them to certain compartments. But most directly it controls them directly, as one controls an automobile with the accelerator and brake.

Glycolysis and the citric acid cycle

the nearly universal glycolysis pathway and citric acid cycle  team up to process food intake. In the glycolysis pathway about a dozen protein enzymes break down the six-carbon sugar known as glucose into two three-carbon molecules. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work.

In addition to breaking down glucose, glycolysis also produces energy-carrying molecules called ATP. These are in constant demand in the cell as they are used wherever energy is needed. Like most pathways, glycolysis is interconnected with other pathways within the cell. The molecular products of glycolysis are used elsewhere and so the rate at which the glycolysis pathway proceeds is important. Too fast and its products won’t be useful, too slow and other pathways have to slow down.

Glycolysis is regulated in a number of ways. The first enzyme in the glycolysis pathway is regulated by its own product. This enzyme alters glucose to form an intermediate product, but if the rest of the pathway is not keeping up then the intermediate product will build up, and this will cause the enzyme to shut down temporarily. The enzyme is designed to be controlled by the presence of its product.

Two other enzymes in the pathway have even more sophisticated regulation. They are sensitive to a number of different molecules which either increase or decrease the enzyme activity. For example, these enzymes are partly controlled by the energy level of the cell. This makes sense since glycolysis helps supply energy to the cell. A good indicator of the cell’s energy level is the relative concentrations of ATP and spent ATP. High levels of ATP indicate a strong energy supply. Hence the enzyme activity is inhibited (and therefore the glycolysis pathway is slowed) when ATP is abundant. But high levels of spent ATP counteract this effect.

How do these molecules control enzyme activity? The molecules are tiny compared to the big enzymes they control. Just as a small key is used to start up and turn off a big truck, so too these small molecules have big effects on their target enzyme. And just as the truck has an ignition lock that can be turned only by the right key, so too the enzyme has several docking sites that are just right for a particular small molecule, such as ATP.

Not only does ATP fit just right into its docking site, but it perturbs the enzyme structure in just the right way so as to diminish the enzyme activity. There is another docking site that only a spent ATP will fit into. And if this occurs then the enzyme structure is again perturbed just right so as to encourage activity and reverse the ATP docking effect.

Glycolysis and the rest of the cell


Glycolysis and the citric acid cycle do not merely create energy for the cell. Just as an oil refinery also produces a range of petroleum products, glycolysis and the citric acid cycle, in addition to producing energy, spin off a series of essential biochemical components needed by the cell. This figure illustrates how these pathways produce nucleotides, lipids, amino acids, cholesterol and other molecules.

In fact glycolysis and the citric acid cycle exist within a complex web of chemical pathways within the cell. These many pathways interaction with each other in many ways.

This design is complex at many levels. At the molecular level, there is the precise control of the protein enzymes. At the pathway level, there is the interaction between the enzymes. And at the cellular level there is interactions between the different pathways. And all of this has nothing in common with evolution’s naïve, religiously-driven, dogma that biology must be one big fluke.



As one evolutionist admitted (one of the textbook authors):


   We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. […]

   Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience. […]

   We have also come to realize that protein assemblies can be enormously complex. … As the example of the spliceosome should make clear, the cartoons thus far used to depict protein machines vastly underestimate the sophistication of many of these remarkable devices. [Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell 92 (1998): 291-294.]


But the dogma remains. Evolutionists insist that evolution must be a fact and they use dozens of religious arguments to make their case. In the next moment they turn around and insist it is all about science. The result is pathetic science, such as the journal paper that tried to explain the citric acid cycle as “evolutionary opportunism.” Religion drives science, and it matters.



1. http://www.reasons.org/articles/why-these-20-amino-acids
2. Arthur L. Weber and Stanley L. Miller, “Reasons for the Occurrence of the Twenty Coded Protein Amino Acids,” Journal of Molecular Evolution 17, no. 5 (1981)
3. http://reasonandscience.heavenforum.org/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins?highlight=amino+acids#3795
4. https://cogmessenger.org/wp-content/uploads/2013/06/Mystery_of_Life_Origin.pdf

Further readings : 

http://oregonstate.edu/instruct/bb350/textmaterials/ch23.html
http://en.wikipedia.org/wiki/Amino_acids
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/amino.html#c1



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Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).


http://www.biocarta.com/pathfiles/h_glycolysispathway.asp




Glucose

Glucose can be made in the body from most types of carbohydrate and from protein, although protein is usually an expensive source of energy.

How do organisms generate energy?

All cells need energy, which they get through ATP, an inherently unstable molecule that must continually be produced.  Though ATP can be produced in different ways, nearly all living cells can harness ATP through glycolysis, the stepwise degradation of glucose, and other sugars, obtained from the breakdown of carbohydrates without the need for molecular oxygen (anaerobic). Glycolysis is an ancient, universal pathway that probably developed ( nice guesswork ) before there was sufficient oxygen in the atmosphere to sustain more effective methods of energy extraction.  When aerobic organisms evolved, they simply added more efficient energy extraction pathways onto glycolysis, breaking down the end products from glycolysis (pyruvate) still further through the tricarboxylic acid cycle.  Yet, aerobic cells can still rely predominantly on glycolysis when oxygen is limiting, such as in hard working muscle cells where glycolysis ends in the production of lactate, causing muscle fatigue.  The aerobic and anaerobic processes are kept separate in eukaryotic cells, with glycolysis occurring in the cytoplasm,

Cytoplasm

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

The cytoplasm comprises cytosol – the gel-like substance enclosed within the cell membrane – and the organelles – the cell's internal sub-structures. All of the contents of the cells of prokaryote organisms (such as bacteria, which lack a cell nucleus) are contained within the cytoplasm.

and the aerobic tricarboxylic acid cycle occurring in the mitochondria.   mitochondria therefore had already to be present !!!

During glycolysis, glucose is broken down in ten steps to two molecules of pyruvate, which then enters the mitochondria where it is oxidised through the tricarboxylic acid cycle to carbon dioxide and water.  Glycolysis can be split into two phases, both of which occur in the cytosol.  Phase I involves splitting glucose into two molecules of glyceraldehyde-3-phosphate (G3P) at the expense of 2 ATP molecules, but allows the subsequent energy-producing reactions to be doubled up with a higher net gain of ATP.  Phase II converts G3P into pyruvate, with the concomitant generation of 4 ATP molecules, giving a net gain of 2 ATP per glucose molecule.  Glycolysis, therefore, provides the cell with a small amount of energy, and, in aerobic cells, provides the starting materials for the complete oxidation of glucose to carbon dioxide and water.

Enzymes of Glycolysis

http://www.ebi.ac.uk/interpro/potm/2004_2/Page2.htm

The different enzymes involved in glycolysis act as kinases, mutases, and dehydrogenases, cleaving enzymes, isomerases or enolases.

Kinases :

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

In biochemistry, a kinase is a type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP,[2] to specific substrates, a process referred to as phosphorylation.

Mutase

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

A mutase is an enzyme of the isomerase class that catalyzes the shifting of a functional group from one position to another within the same molecule. Examples of this are bisphosphoglycerate mutase, which appears in red blood cells and phosphoglycerate mutase, which acts in glycolysis. In glycolysis, it changes 3-phosphoglycerate to 2-phosphoglycerate. In particular it moves phosphate groups within a single molecule, for instance: phosphoglycerate mutase.

Dehydrogenases

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

A dehydrogenase (also called DHO in the literature) is an enzyme that oxidizes a substrate by a reduction reaction that transfers one or more hydrides (H−) to an electron acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN.

They act in concert to split or rearrange the intermediates, to add on phosphate groups, and to move those phosphate groups onto ADP to make ATP.  Several of the reactions involve the phosphorylation of intermediates, which is important not only for the production of ATP from ADP, but also as a useful handle on the substrate for enzyme binding, to trap intermediates within the cell, and to drive pathways in one direction by making phosphorylation and dephosphorylation reactions irreversible.  The different enzymes have been split into two groups, those in phase I and those in phase II, simply for convenience.

Hexokinase (EC 2.7.1.1)

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

A hexokinase is an enzyme that phosphorylates hexoses (six-carbon sugars), forming hexose phosphate. In most organisms, glucose is the most important substrate of hexokinases, and glucose-6-phosphate the most important product.

Genes that encode hexokinase have been discovered in every domain of life, and exist among a variety of species that range from bacteria, yeast, and plants to humans and other vertebrates

Most bacterial hexokinases are approximately 50 kD in size. Multicellular organisms such as plants and animals often have more than one hexokinase isoform. Most are about 100 kD in size and consist of two halves (N and C terminal), which share much sequence homology.

Phosphoglucose_isomerase


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

Glucose-6-phosphate isomerase (alternatively known as phosphoglucose isomerase or phosphohexose isomerase) is an enzyme that catalyzes the conversion of glucose-6-phosphate into fructose 6-phosphate in the second step of glycolysis.

http://www.ncbi.nlm.nih.gov/pubmed/19688275

In this study, a 2,338 bp of full-length cDNA cloned using rapid amplification of cDNA end (RACE) technique contained an open reading frame (ORF) of 1,980 bp encoding 660 amino acids, which has a predicted molecular weight of 73.3 kD and pI of 6.22 and shares high homology with other organisms.

Phosphofructokinase

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

Phosphofructokinase is a kinase enzyme that phosphorylates fructose 6-phosphate in glycolysis.

PFK is about 300 amino acids in length, and structural studies of the bacterial enzyme have shown it comprises two similar (alpha/beta) lobes: one involved in ATP binding and the other housing both the substrate-binding site and the allosteric site (a regulatory binding site distinct from the active site, but that affects enzyme activity).

Fructose-bisphosphate_aldolase

http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase

Fructose-bisphosphate aldolase (EC 4.1.2.13), often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP).


PHASE II:  The enzymes in detail

http://www.ebi.ac.uk/interpro/potm/2004_2/Page3.htm

The second phase of glycolysis involves the extraction of energy in the form of 4 ATP per molecule of glucose, a net gain of 2 ATP molecules.  The product of glycolysis, pyruvate, can then be further broken either aerobically ( to carbon dioxide and water through the TCA cycle) or anaerobically (to lactate or alcohol).


Glyceraldehyde 3-phosphate dehydrogenase  (EC 1.2.1.12)

Catalyses:  Glyceraldehyde-3-phosphate (G3P) +NAD+ + Pi à 1,3-Bisphosphoglycerate (1,3BPG) + NADH + H+


Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis by reversibly catalysing the oxidation and phosphorylation of G3P to the energy-rich intermediate 1,3BPG.  NAD+ is a co-substrate for this reaction.

GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location.  For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis.  The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription.  The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself.

GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington’s disease, Alzheimer’s disease, Parkinson’s disease and Machado-Joseph disease through stretches encoded by their CAG repeats.  Abnormal neuronal apoptosis is associated with these diseases.  Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins.

Phosphoglycerate kinase (EC 2.7.2.3)

Catalyses:  1,3-Bisphosphoglycerate (1,3BPG) + ADP à 3-Phosphoglycerate (3PG) + ATP

  Phosphoglycerate kinase (PGK) is an enzyme that reversibly catalyses the formation of ATP to ADP, using one of the high-energy phosphate groups from 1,3BPG.  The reaction forms two ATP molecules per glucose (one per 1,3BPG molecule), which compensates for the expenditure of 2 ATP in phase I of glycolysis.  The ATP is made by substrate-level phosphorylation, where a phosphate group is transferred from 1,3BPG directly to ADP.  This reaction is essential in most cells for the generation of ATP in aerobes, for fermentation in anaerobes and for carbon fixation in plants.

Deficiencies in PGK are associated with haemolytic anaemia, myopathy, central nervous system disorder and growth retardation.


Phosphoglycerate mutase (EC 5.4.2.1)


Catalyses:  3-Phosphoglycerate (3PG) à 2-Phosphoglycerate (2PG)

Phosphoglycerate mutase (PGAM) catalyses the transfer of the phospho group from the C3 position to the C2 position, in preparation for the synthesis of ATP.  PGAM enzymes from different sources exhibit different reaction mechanisms.  For instance, some PGAM enzymes (vertebrates, fungi, certain bacteria) use 2,3-bisphophoglycerate as a cofactor to phosphorylate a serine residue to prime the reaction, whereas other PGAM enzymes (plants, certain invertebrates, algae, certain bacteria) carry out intramolecular phosphoryl group transfer via an active site residue without the need of a cofactor.

Deficiencies in PGAM can cause acute muscle dysfunction with exercise intolerance and muscle breakdown.


Enolase (EC 4.2.1.11)

Catalyses:  2-Phosphoglycerate (2PG) à Phosphoenolpyruvate (PEP) + H2O

Enolase (phosphopyruvate hydratase) is an essential glycolytic enzyme that catalyses the reversible dehydration of 2-phosphoglycerate to the high-energy intermediate phosphoenolpyruvate.  Enolase is strongly inhibited by fluoride ions, which forms a fluorophosphate complex with magnesium at the active site.  In vertebrates, there are 3 different, tissue-specific isozymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue.  The functional enzyme exists as homo- or hetero-dimers of the different isozymes.  In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer.

Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke.  Several tumour cells have also been found positive for neuron-specific enolase.  Beta-enolase deficiency is associated with glycogenosis type XIII defect.

Pyruvate kinase (EC 2.7.1.40)

Catalyses:  Phosphoenolpyruvate (PEP) + ADP à Pyruvate + ATP

Pyruvate kinase (PK) catalyses the final step in glycolysis, the conversion of PEP to pyruvate with the concomitant transfer of the high-energy phosphate group from PEP to ADP, thereby generating ATP.  PK requires both magnesium and potassium for activity.  In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes.

PK helps control the rate of glycolysis, along with phosphofructokinase and hexokinase.  PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions.  The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted.  L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme.  M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver.

The pyruvate produced by PK feeds into a number of different metabolic pathways.  Under aerobic conditions, pyruvate can be transported to the mitochondria, where it enters the TCA cycle and is further broken down to produce considerably more ATP through oxidative phosphorylation.  Alternatively, pyruvate can be anaerobically reduced to lactate in cells lacking mitochondria, or under hypoxic conditions, such as found in hard working muscle tissues.  Other by-products of anaerobic breakdown of pyruvate include ethanol during fermentation by yeast

pentose phosphate pathway

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

It's main role today is to produce ribose 5-phosphate for nucleic acid synthesis.

The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose monophosphate shunt) is a process that generates NADPH and pentoses (5-carbon sugars). There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon sugars. This pathway is an alternative to glycolysis. While it does involve oxidation of glucose, its primary role is anabolic rather than catabolic. For most organisms, it takes place in the cytosol; in plants, most steps take place in plastids.

anabolic and catabolic

In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly. Because of the many chemicals (a.k.a. "metabolites") that may be involved, metabolic pathways can be quite elaborate. In addition, numerous distinct pathways co-exist within a cell. This collection of pathways is called the metabolic network. Pathways are important to the maintenance of homeostasis within an organism. Catabolic (break-down) and Anabolic (synthesis) pathways often work interdependently to create new biomolecules as the final end-products.

The primary results of the Pathway are:

   The generation of reducing equivalents, in the form of NADPH, used in reductive biosynthesis reactions within cells. (e.g. fatty acid synthesis)
   Production of ribose-5-phosphate (R5P), used in the synthesis of nucleotides and nucleic acids.
   Production of erythrose-4-phosphate (E4P), used in the synthesis of aromatic amino acids.

Nicotinamide adenine dinucleotide phosphate, abbreviated NADP+ or, in older notation, TPN (triphosphopyridine nucleotide), is a coenzyme used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent.

In plants

In photosynthetic organisms, NADPH is produced by ferredoxin-NADP+ reductase in the last step of the electron chain of the light reactions of photosynthesis. It is used as reducing power for the biosynthetic reactions in the Calvin cycle to assimilate carbon dioxide. It is used to help the carbon dioxide turn into glucose.

NADPH

Nicotinamide adenine dinucleotide phosphate, abbreviated NADP+ or, in older notation, TPN (triphosphopyridine nucleotide), is a coenzyme used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent.
NADPH is the reduced form of NADP+. NADP+ differs from NAD+ in the presence of an additional phosphate group on the 2' position of the ribose ring that carries the adenine moiety.

citric acid cycle

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

The citric acid cycle — also known as the tricarboxylic acid cycle (TCA cycle), or the Krebs cycle,— is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetate derived from carbohydrates, fats and proteins into carbon dioxide and chemical energy in the form of adenosine triphosphate (ATP). In addition, the cycle provides precursors of certain amino acids as well as the reducing agent NADH that is used in numerous other biochemical reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically.






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://www.biu.ac.il/LS/People/staff/Berman/n2review_2003.pdf

The nitrogen cycle of Earth is one of the most critical yetpoorly understood biogeochemical cycles. Current estimates of global N2 fixation are∼240 Tg N y−1with a marine contribution of 100–190 Tg N y−1. Of this, a single non-heterocystous genus,Trichodesmium sp. contributes approx-imately∼100 Tg N y−1(Capone pers. comm.).

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

Trichodesmium, also called sea sawdust, is a genus of filamentous cyanobacteria. They are found in nutrient poor tropical and subtropical ocean waters (particularly around Australia and the Red Sea, where they were first described by Captain Cook). Trichodesmium is a diazotroph; that is, it fixes atmospheric nitrogen into ammonium, usable also for other organisms. Trichodesmium is the only known diazotroph able to fix nitrogen in day light under aerobic conditions without the use of heterocysts.

Heterocysts are specialized nitrogen-fixing cells formed during nitrogen starvation by some filamentous cyanobacteria, such as Nostoc punctiforme, Cylindrospermum stagnale, and Anabaena sphaerica. They fix nitrogen from dinitrogen (N2) in the air using the enzyme nitrogenase, in order to provide the cells in the filament with nitrogen for biosynthesis.


http://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445

To date, scientists have discovered more than five hundred amino acids in nature, but only twenty-two participate in translation.


What Is an Amino Acid Made Of?

As implied by the root of the word (amine), the key atom in amino acid composition is nitrogen. 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). 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. All organisms contain the enzymes glutamate dehydrogenase and glutamine synthetase, which convert ammonia to glutamate and glutamine, respectively. Amino and amide groups from these two compounds can then be transferred to other carbon backbones by transamination and transamidation reactions to make amino acids. Interestingly, glutamine is the universal donor of amine groups for the formation of many other amino acids as well as many biosynthetic products. Glutamine is also a key metabolite for ammonia storage. All amino acids, with the exception of proline, have a primary amino group (NH2) and a carboxylic acid (COOH) group. They are distinguished from one another primarily by , appendages to the central carbon atom.

the key atom in amino acid composition is nitrogen.

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.


Nitrogenase is the only family of enzymes capable of breaking this bond

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

The enzyme is composed of the heterotetrameric MoFe protein that is transiently associated with the homodimeric Fe protein. Electrons for the reduction of nitrogen are supplied to nitrogenase when it associates with the reduced, nucleotide-bound homodimeric Fe protein. The heterocomplex undergoes cycles of association and disassociation to transfer one electron, which is the rate-limiting step in nitrogen reduction[citation needed]. ATP supplies the energy to drive the transfer of electrons from the Fe protein to the MoFe protein. The reduction potential of each electron transferred to the MoFe protein is sufficient to break one of dinitrogen's chemical bonds, though it has not yet been shown that exactly three cycles are sufficient to convert one molecule of N2 to ammonia. Nitrogenase ultimately bonds each atom of nitrogen to three hydrogen atoms to form ammonia (NH3), which is in turn bonded to glutamate to form glutamine. The nitrogenase reaction additionally produces molecular hydrogen as a side product.

http://www.spacedaily.com/news/life-03m.html

Nitrogen fixation is one of the most interesting biological processes because it's so difficult to do chemically. Nitrogenase is a very complex enzyme system that actually breaks molecular nitrogen's triple bond,"

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, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved.[/justify]
[/b]


http://www.chem.utoronto.ca/coursenotes/GTM/JM/N2start.htm

Nitrogenase genes are distributed throughout the prokaryotic kingdom, including representatives of the Archaea as well as the Eubacteria and Cyanobacteria.

The enzyme nitrogenase is found in certain bacteria and blue-green algae, which can reduce N2 to NH3 (nitrogen fixation). Some of these bacteria are free-living while others are symbiotic (in the anaerobic environment of roots of legume plants). This bacterial reaction is the key step in the nitrogen cycle, which maintains a balance between two reservoirs of the nitrogen compounds: the Earths atmosphere and the biosphere. The plants cannot extract nitrogen directly from the atmosphere.

Much could be learned from the synthetic models for nitrogenase's cluster and cofactors (their function, mechanism of dinitrogen reduction, possible applications as industrial catalysts etc). However, the design and preparation of such compounds presents a major challenge for synthetic chemists. The most notable examples, described below, come from Holm's research group. Even though nitrogenase has been extensively studied many important questions still remain unanswered, for example: How is the substrate (dinitrogen) binding to the MoFe cofactor? What is the mechanism of dinitrogen reduction?

http://chemwiki.ucdavis.edu/Wikitexts/UC_Davis/UCD_Chem_124A%3A_Berben/Nitrogenase/Nitrogenase_1

There are numerous types of enzymes, complexes, and oNitrogenase.pngther material that operate in living organisms and can be important to their survival. Nitrogenase, shown in Figure 1, is one enzyme that is produced by certain types of bacteria and is vital to their existence and growth. 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” [3]. 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 Nitrogenase crystal structure.pngcreate 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 [6]. 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 [4]. 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.

Many details have been discovered over time about the functioning of nitrogenase, but there has yet to a complete agreement on the structure of nitrogenase. The iron-molybdenum cofactor center of the nitrogenase Molecule structure.pngenzyme consists of iron, sulfur, molybdenum, a homocitrate molecule, a histadine amino acid and a cysteine amino acid [7].

The restrictive functionality of nitrogenase makes it only possible for anaerobic organisms to utilize nitrogenase.

http://creation.com/the-molecular-sledgehammer

The molecular sledgehammer

The amazing story of how scientists struggled for years to duplicate an important bit of chemistry.

Great human inventions are usually recognized, with due fame and honour given to those whose work they are. The awarding of the Nobel Prizes is a yearly reminder to us that great achievements are worthy of recognition and reward.

The light-harnessing ability of the chlorophylls (the chemicals that utilize the sun's energy in green plants) might also find a place of honour. Another tiny but marvellous bit of biochemistry which could be nominated to such a position is a mechanism which might be termed ‘the molecular sledgehammer’.

To appreciate the work done by this ‘sledgehammer’, it is important to understand the role of the element nitrogen in the living world. The two main constituents of our atmosphere, oxygen (21%) and nitrogen (78%), both play important roles in the makeup of living things. Both are integral parts of the amino acids which join together in long chains to make all proteins, and of the nucleotides which do the same thing to form DNA and RNA. Getting elemental oxygen (O2) to split apart into atoms and take part in the reactions and structures of life is not hard; in fact, oxygen is so reactive that keeping it from getting into where it's not wanted becomes the more challenging job. However, elemental nitrogen poses the opposite problem. Like oxygen, it is diatomic (each molecule contains two N atoms) in its pure form (N2); but, unlike oxygen, each of its atoms is triple-bonded to the other. 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?

Perhaps this problem can be better appreciated by putting it into terms of human engineering. We need nitrogen for our bodies, to form amino acids and nucleic acids. We must get this nitrogen from our food, whether plant or animal. The animals we eat must rely on plant sources, and the plants must get it from the soil. Nitrogen forms the basis for most fertilizers used in agriculture, both natural and artificial. Natural animal wastes are rich in nitrogen, and it is largely this property that makes them enrich the soil for plant growth. In the late 1800s, a growing population created a great need for nitrogen compounds that could be used in agriculture. At the time, the search for more usable nitrogen was considered a race to stave off Malthusian1 predictions of mass starvation as population outgrew food supply. So chemists wrestled for years with the problem of how to convert the plentiful nitrogen in the air into a form suitable for use in agriculture.

Since naturally occurring, mineable deposits of nitrates were rare, and involved transportation over large distances, an industrial process was greatly needed. Finally, around 1910, a German, Fritz Haber, discovered a workable large-scale process whereby atmospheric nitrogen could be converted to ammonia (NH3). His process required drastic conditions, using an iron-based catalyst with around 1000oF (540oC) heat and about 300 atmospheres of pressure. Haber was given the 1918 Nobel Prize for chemistry because of the great usefulness of his nitrogen-splitting process to humanity.

One might ask, if elemental gaseous nitrogen is such a tough nut to crack, how do atoms of nitrogen ever get into the soil naturally? Some nitrogen is split and added to the soil by lightning strikes. Again, it is a reminder of the force necessary to split the NN bond that the intense heat and electricity of lightning are needed to do it. Still, only a relatively minor amount of nitrogen is added to the Earth’s topsoil yearly by thunderstorms. How is the remainder produced?

The searching chemists of a century ago did not realize that an ingenious method for cracking nitrogen molecules was already in operation. This process did not require high temperatures or pressures, and was already working efficiently and quietly to supply the Earth's topsoil with an estimated 100 million tons of nitrogen every year. This process’ inventor was not awarded a Nobel Prize, nor was it acclaimed with much fanfare as the work of genius that it is. This process is humbly carried on by a few species of the ‘lowest’ forms of life on Earth—bacteria and blue-green algae (Cyanobacteria).

Some of these tiny yet amazingly sophisticated organisms live in symbiosis (mutually beneficial ‘living together’) with certain ‘higher’ plants, known as legumes. The leguminous plants include peas, soybeans and alfalfa, long valued as crops because of their unique ability to enrich the soil. The microbes invade their roots, forming visible nodules in which the process of nitrogen cracking is carried on.

Modern biochemistry has given us a glimpse of the enzyme system used in this process. The chief enzyme is nitrogenase, which, like hemoglobin, is a large metalloprotein complex.2 Like Fritz Haber’s process, and like catalytic converters in cars today, it uses the principle of metal catalysis. However, like all biological enzymatic processes, it works in a more exact and efficient way than the clumsy chemical processes of human invention. Several atoms of iron and molybdenum are held in an organic lattice to form the active chemical site. 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.

One author summed up the situation well by remarking, ‘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.’4 If one merely substitutes the name of God for the word 'nature', the real picture emerges.

Creationist Christians are often accused of having the same easy answer for any question about specific origin of things in nature: the 'God of the gaps' did it. But this criticism can be easily turned around. What answers do evolutionists give to explain the origin of microscopic marvels like the molecular sledgehammer? They can't explain them scientifically, so they resort to a standard liturgy, worshipping the power of blind chance and natural selection.

One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering. To believe that it was worked out by a wise and caring Creator, who provides all necessary things for the life of His creatures, is far more reasonable than the mystical evolutionary alternative. One grows tired of hearing the same monotonous mantra that ‘we know evolution did it, we just don’t know how.’


How can natural processes and mechanisms  write a book ? compose a partiture ? write a morse code, or a computer code ? how can physics write a dna code to  make the machinery to produce the machines ( enzyme proteins made of amino acids ) , many of which operate at the same time and in the same small volume of the cytosol. By their catalytic action, these enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. . The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. The carbon backbones come from the glycolytic pathway, the pentose phosphate pathway, or the citric acid cycle, all needing complex enzyme catalytic pathways. A living cell, even the most primitive ones, contain thousands of these enzymes, many of which operate at the same time and in the same small volume of the cytosol( the liquid inside the cell ) .  Not only do you need a encoder to produce the coded information to make the enzymes, but you need the machinery all in place right since the beginning : how could otherwise the machinery be built in a step up fashion, one enzyme after the other, if the end product is only made with all the machines in place and working in a ensemble, and the end product are actually the building blocks of these machines, that make amino acids and ATP ? that is a interdependent system. If one enzyme is not in place, the whole machinery will not work. No amino acids, no ATP ( the fuel in the cell ), no life. 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. You can see the glycolytic pathway in the video :


http://www.youtube.com/watch?v=hDq1rhUkV-g

http://christiananswers.net/q-crs/abiogenesis.html

Some bacteria, specifically phototrophs and lithotrophs, contain all the metabolic machinery necessary to construct most of their growth factors (amino acids, vitamins, purines and pyrimidines) from raw materials (usually O2, light, a carbon source, nitrogen, phosphorus, sulfur and a dozen or so trace minerals). They can live in an environment with few needs but first must possess the complex functional metabolic machinery necessary to produce the compounds needed to live from a few types of raw materials. This requires more metabolic machinery in order to manufacture the many needed organic compounds necessary for life.



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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........

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The short argument :

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.

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

The long argument :

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.


http://everything2.com/title/nitrogen+fixation

The cofactor holds the molecular nitrogen in place, and then bombards the metal atoms with so much electrons that they are able to pull the molecular nitrogen apart. The full description of what happens is more complicated, of course. The reaction takes so much energy, and produces so many toxic products, that it would probably be lethal inside of the cells of a higher plant, but the bacteria are able to produce the nitrogen without too many ill effects.

http://home.iprimus.com.au/nielsens/nitrogen.html

It's really marvelous! What a lightening does with a big bang and with a huge discharge of energy, these tiny microorganisms do the same without fuss. They can take the biologically useless nitrogen from the atmosphere, break it apart, and convert it to nitrogen compounds that can be used by other living organisms. Isn't it a clever solution.

What is most incredible  is the fact that small bacteria, using nothing but an organic protein with some iron and a molybdenum atom, are able to do something that otherwise requires the immense energy of lightning flashes or heavy industrial processes. It also says something about the mutual elegance and inelegance of life on earth. While almost all of the earth's plants are busy breaking apart and using the vanishingly tiny amount of carbon dioxide in the atmosphere, the just as vital task of breaking the gigantic amount of atmospheric nitrogen is left to a small amount of bacteria living inside of the roots of several plants. And the bacteria does that through a Rube Goldberg protein that utilizes a complicated core of metal atoms. "Molybdenum" may not be high on most people's list of necessities for life, and yet it is. (Almost) every nitrogen atom in your body was once next to a molybdenum atom inside a bacteria inside a pea plant).



Nitrogen becomes available in following ways:

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

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 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.

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http://www.rationalskepticism.org/creationism/origin-of-amino-acids-t42989.html

Before asking about how the genetic code arose, we need to elucidate the origin of amino acids.

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

problem 1 :

In amino acid production, one encounters an important problem in biosynthesis, namely stereochemical control.

homochirality :

RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, FASEB Journal (Federation of American Societies for Experimental Biology), 12: 503-507 (1998)

It is possible that steric interactions of the bulky dinitrobenzoyl group with nitrogenous bases may have been involved in the reversal of selectivity, since enantiomeric excesses decreased from about 60% for polypurines to only 35% for polypyrimidine nucleotides; when the smaller N carboxy-anhydrides were used, no stereoselectivity was observed.

35% enantiomeric excess of L-amino acids is not nearly enough to produce any reasonably-sized protein.

:popcorn:

Problem no. 2

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/scitable/topicpag ... s-14568445

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/Wikitexts/U ... rogenase_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........

Follow will the glycolytic pathway.

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