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?
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.
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). 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).
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.
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.
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 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.
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 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.
The carbon skeletons come from intermediates of glycolysis, the pentose phosphate pathway and the citric acid cycle.
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.
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 , 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
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.
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)
Further readings :
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