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Abiogenesis enigma: Protein’s origin

Proteins

As you might know, proteins are one of the major “building blocks” of cells; there’s up to 10.000 different types of proteins, all manufactured inside each cell. Abiogenesis theorists  obviously supports the view that these molecules have arisen “by chance”, in a prebiotic world, billion years ago, however, to date, they have absolutely no clue about it, as we can read from this article:

“Proteins are the most complex chemicals synthesized in nature and must fold into complicated three-dimensional structures to become active. This poses a particular challenge in explaining their evolution from non-living matter. So far, efforts to understand protein evolution have focused on domains, independently folding units from which modern proteins are formed. Domains however are themselves too complex to have evolved de novo in an abiotic environment. We think that domains arose from the fusion of shorter, non-folding peptides, which evolved as cofactors supporting a primitive, RNA-based life form (the ‘RNA world’).” 1

So, why is it so complicated to explain its origin? Despite the often repeated innuendo that life and all of its components has “assuredly” originated through natural means, the clear failure of scientists to solve this puzzle can be easily explained by some truths about proteins, its synthesis, structure and so on. After that, no one can reasonably take its abiogenetic origin as logically granted. These truths also explain without shadow of doubt the intriguing fact that absolutely no single protein (even the lesser one, composed of only 8 amino acids) has ever been observed to appear anywhere in the world, outside the cells and high-tech labs, of course!

What’s a protein?

“Proteins are large biological molecules consisting of one or more chains of amino acids. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactionsreplicating DNAresponding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in folding of the protein into a specific three-dimensional structure that determines its activity.

A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids;” 2

Talking about amino acids, we’d like to recall another crucial problem for abiogenesis: The absence of self-occurring homochiral mixtures. As it has been told in a previous article, the laws of thermodynamics obliges the occurrence of racemic mixtures, ever:

“The left and right handed forms have identical free energy (G), so the free energy difference (ΔG) is zero. The equilibrium constant for any reaction (K) is the equilibrium ratio of the concentration of products to reactants. The relationship between these quantities at any Kelvin temperature (T) is given by the standard equation:

K = exp (–ΔG/RT)

where R is the universal gas constant (= Avogadro’s number x Boltzmann’s constant k) = 8.314 J/K.mol.

For the reaction of changing left-handed to right-handed amino acids (L → R), or the reverse (R → L), ΔG = 0, so K = 1. That is, the reaction reaches equilibrium when the concentrations of R and L are equal; that is, a racemate is produced.”

Therefore, any abiogenetic theorist has this astounding problem to deal with from the very beginning; without homochiral monomers, we can have zero possibility of a ‘magic’ protein self-assembling…

 

Protein synthesis

 

It’s quite uncanny that intelligent people with advanced knowledge on the subject might attempt to conceive hypothesis of such molecules originating spontaneously, in the wild and morbid inorganic environment, because for cells to build proteins, an intricate, complex and laborious process must take place!

 

 

First, genetic information is needed:

“Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid (for example AUG (adenineuracilguanine) is the code for methionine).”

 

Many proteins use more that one of the 64 possible codons to be built. Moreover, that specific genetic code must be first translated, transcribed:

“Genes encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of Post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome.”

Oh great, a bit complicated, isn’t it? Please, read the Wikipedia article referring to the messenger RNA, for further comprehension of what it is, its manufacturing, composition, etc; all of which adds up more complexity for the protein origin’s explanation.

 

 

The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase “charges” the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus.[6]

The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa). Yeast proteins are on average 466 amino acids long and 53 kDa in mass.[5] The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.[8]

 

Phew! How complicated! You may ask now: are we finally done? And I reply you: Huh, nope! Now that the ribosome, together with the rRNA and more than 50 other proteins, has finally finished the process, a protein is formed. However, it is always found in a  random coil shape. So what? This shape is mostly useless for its usage on organism, as we can read:

Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the neighbouring figure). 3

In that randomly coiled shape, the protein is highly unstable, breakable, useless for cell building, so, for proper biological use and better stability, the protein folding process must take place. This 3D-shape is known as the native state.

The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded.[4] Failure to fold into native structure generally produces inactive proteins, but in some instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins.[5] Many allergies are caused by incorrect folding of some proteins, for the immune system does not produce antibodies for certain protein structures.[6]

Another importance of the protein folding is:

 

Minimizing the number of hydrophobic side-chains exposed to water is an important driving force behind the folding process.[9] Formation of intramolecular hydrogen bonds provides another important contribution to protein stability.[10] 

 

And how does the folding occurs?

 

 

The amino-acid sequence of a protein determines its native conformation.[7] A protein molecule folds spontaneously during or after biosynthesis. While these macromolecules may be regarded as “folding themselves“, the process also depends on the solvent (water or lipid bilayer),[8] the concentration of salts, the pH, the temperature, the possible presence of cofactors and of molecular chaperones.

The process of folding often begins co-translationally, so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still beingsynthesized by the ribosome. Specialized proteins called chaperones assist in the folding of other proteins.

Although most globular proteins are able to assume their native state unassisted, chaperone-assisted folding is often necessary in the crowded intracellular environment to prevent aggregation; chaperones are also used to prevent misfolding and aggregation that may occur as a consequence of exposure to heat or other changes in the cellular environment.

There are two models of protein folding that are currently being confirmed: The first: The diffusion collision model, in which a nucleus is formed, then the secondary structure is formed, and finally these secondary structures are collided together and pack tightly together. The second: The nucleation-condensation model, in which the secondary and tertiary structures of the protein are made at the same time. Recent studies have shown that some proteins show characteristics of both of these folding models.

The essential fact of folding, however, remains that the amino acid sequence of each protein contains the information that specifies both the native structure and the pathway to attain that state. Folding is a spontaneous process independent of energy inputs from nucleoside triphosphates. The passage of the folded state is mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, and van der Waals forces, and it is opposed by conformational entropy.

Only after the folding process, we have an useful, stable protein, with a properly designed shape with its up to four layers, so that the molecule can perform its biological function.

But, remember, many conditions and external factors can destroy proteins, such as hydrolysis (it’s a slow, but ceaseless process, because proteins are metastable, hydrophobic) and others:

Under some conditions proteins will not fold into their biochemically functional forms. Temperatures above or below the range that cells tend to live in will cause thermally unstableproteins to unfold or “denature” (this is why boiling makes an egg white turn opaque). High concentrations of solutes, extremes of pH, mechanical forces, and the presence of chemical denaturants can do the same.

A fully denatured protein lacks both tertiary and secondary structurel. Under certain conditions some proteins can refold; however, in many cases, denaturation is irreversible.[15] Cells sometimes protect their proteins against the denaturing influence of heat with enzymes known as chaperones or heat shock proteins, which assist other proteins both in folding and in remaining folded. Some proteins never fold in cells at all except with the assistance of chaperone molecules, which either isolate individual proteins so that their folding is not interrupted by interactions with other proteins or help to unfold misfolded proteins, giving them a second chance to refold properly. This function is crucial to prevent the risk of precipitation into insoluble amorphous aggregates.

 

For a further an in-depth study about different factors capable of disrupting proteins, read the following articles:

https://en.wikipedia.org/wiki/Protein_biosynthesis

http://creation.com/native-folds-in-polypeptide-chains-1 (a series of 6 parts)

 

To conclude our observation, it’s impossible not to be sceptic of any theoretic proposition that claims self-caused origin of proteins, because it turns out that science unveiled tons of facts that easily prevent any possibility of such proposed scenario:

 

-Absence of homochiral monomers forming in the environment;

-Necessity of genetic specific information;

-Need for an highly controlled ambient, with proper Ph level, temperature, absence of mechanical forces that may easily damage, disrupt the protein, toxins, etc; 

-Need for specific methods to protect the protein against hydrolysis, oxidation;

-Necessity of having 50 other types of protein already manufactured to help on the protein synthesis;

 

The question raises: how in the world could such a specific set of conditions be found in a prebiotic Earth? Such condition can only be barely found in a first-class laboratory, driven by qualified and experienced scientists!

You might as well enjoy watching this short video talking about protein synthesis:

 

References

1. <http://www.eb.tuebingen.mpg.de/research/departments/protein-evolution/protein-evolution.html>

2. <https://en.wikipedia.org/wiki/Protein>

3. <https://en.wikipedia.org/wiki/Protein_folding>

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Oh, homochirality…

Naturalistic theories have many insurmountable problems, dilemmas, if not for their anti-theistic commitment, many brilliant, renowned persons would never bother to conceive such a stupid wishful thinking, because the odds for a mere protein to form itself without intelligent influence are astronomical, in fact, impossible! Read now some scientific facts against the homochirality to happen by chance.

An organism is composed of countless molecules, the “building blocks” of life. Nearly all biological polymers must be homochiral (all its component monomers having the same handedness. Another term used is optically pure or 100 % optically active) to function. All amino acids in proteins are ‘left-handed’, while all sugars in DNA and RNA, and in the metabolic pathways, are ‘right-handed’. Whether or not a molecule or crystal is chiral is determined by its symmetry. A molecule is achiral (non-chiral) if and only if it has an axis of improper rotation, that is, an n-fold rotation (rotation by 360°/n) followed by a reflection in the plane perpendicular to this axis maps the molecule on to itself. Thus a molecule is chiral if and only if it lacks such an axis.

A 50/50 mixture of left- and right-handed forms is called a racemate or racemic mixture. Racemic polypeptides could not form the specific shapes required for enzymes, because they would have the side chains sticking out randomly. Also, a wrong-handed amino acid disrupts the stabilizing α-helix in proteins. DNA could not be stabilised in a helix if even a single wrong-handed monomer were present, so it could not form long chains. This means it could not store much information, so it could not support life.

To begin with, it’s a well known FACT that homochiral molecules are never found outside a cell (except, of course, in labs, under the human, therefore intelligent,  manipulation). Why? Laws of physics, dear!

consequence of the Laws of Thermodynamics. The left and right handed forms have identical free energy (G), so the free energy difference (ΔG) is zero. The equilibrium constant for any reaction (K) is the equilibrium ratio of the concentration of products to reactants. The relationship between these quantities at any Kelvin temperature (T) is given by the standard equation:

K = exp (–ΔG/RT)

where R is the universal gas constant (= Avogadro’s number x Boltzmann’s constant k) = 8.314 J/K.mol.

For the reaction of changing left-handed to right-handed amino acids (L → R), or the reverse (R → L), ΔG = 0, so K = 1. That is, the reaction reaches equilibrium when the concentrations of R and L are equal; that is, a racemate is produced. A famous textbook correctly stated:

‘Synthesis of chiral compounds from achiral reagents always yields the racemic modification.’ and ‘Optically inactive reagents yield optically inactive products.’ (Morrison, R.T. and Boyd, R.N., 1987. Organic Chemistry, 5th ed. Allyn & Bacon Inc. p.150)

It also states:

‘We eat optically active bread & meat, live in houses, wear clothes, and read books made of optically active cellulose. The proteins that make up our muscles, the glycogen in our liver and blood, the enzymes and hormones … are all optically active. Naturally occurring substances are optically active because the enzymes which bring about their formation … are optically active. As to the origin of the optically active enzymes, we can only speculate’

Nonetheless, they (the naturalists) are “sure” of the casual origin of everything… They just can’t explain HOW could it happen, nor can they show the farthest, slightest evidence of the nothingness creating things that violate its laws, such as homochirality! English biologist John Maddox called it “an intellectual thunderbolt that natural proteins should contain only the left-handed forms of the amino acids.”. But it was not for the lack of efforts and guesswork. The famous Oparin once went on to say:

“The probability of the formation of one antipode or the other is therefore the same. As the law of averages applies to chemical reactions the appearance of an excess of one antipode is very improbable, and, in fact, we never encounter it under the conditions of non-living nature and in laboratory syntheses . . . .
In living organisms, on the contrary, the amino acids of which naturally occurring proteins are made always have the left-handed configuration. . . . This ability of protoplasm selectively to synthesize and accumulate one antipode alone is called the asymmetry of living material. It is a characteristic feature of all organisms without exception but is absent from inanimate nature. 

Pasteur pointed out this fact as follows: “This great character is, perhaps, the only sharp dividing line which we can draw at present between the chemistry of dead and living nature.”” (A. I. Oparin, Life, Its Nature, Origin and Development (New York: Academic Press, 1961), pp. 59, 60)

Ever since, many theories were proposed, in an effort to solve this unbelievable puzzle, but they have all failed, as we’re going to see some now.

How can we separate the left from the right?

It’s not that simple! First of all, you need of intelligence behind the process… To resolve a racemate, another homochiral substance must be introduced. The procedure is explained in any organic chemistry textbook. The idea is that right-handed and left-handed substances have identical properties, except when interacting with other chiral phenomena. The analogy is that our left and right hands grip an achiral (non-chiral) object like a baseball bat equally, but they fit differently into a chiral object like a left-handed glove. Thus to resolve a racemate, an organic chemist will usually use a ready-made homochiral substance from a living organism.

However, this does not solve the mystery of where the optical activity in living organisms came from in the first place. An world conference on ‘The Origin of Homochirality and Life’ made it clear that the origin of this handedness is a complete mystery to evolutionists (Cohen, J., 1995. Science, 267:1265–1266). The probability of forming one homochiral polymer of N monomers by chance = 2–N. For a small protein of 100 amino acids, this probability = 2–100 = 10–30. Note, this is the probability of any homochiral polypeptide. The probability of forming a functional homochiral polymer is much lower, since a precise amino acid sequence is required in many places.

A further problem is that homochiral biological substances racemize in time. This is the basis of the amino acid racemization dating method. Its main proponent is Jeffrey Bada of the Scripps Institution of Oceanography in La Jolla, California(Bada, J.L., Luyendyk, B.P. and Maynard, J.B., 1970. Science, 170:730–732). As a dating method, it is not very reliable, since the racemization rate is strongly dependent on temperature and pH, and depends on the particular amino acid (Gish, D.T., 1975.  Impact series #23, ICR). Racemization is also a big problem during peptide synthesis and hydrolysis. It shows that the tendency of undirected chemistry is towards death, not life.

Beta decay and the weak force

β-decay is one form of radioactive decay, and it is governed by one of the four fundamental forces of nature, the weak force. This force has a slight handedness, called parity violation, so some theorists thought β-decay could account for the chirality in living organisms. However, the weak force is aptly named—the effect is minuscule—a long way from producing the required 100 % homochirality. One specialist in the chirality problem, organic chemist William Bonner, professor emeritus at Stanford University, said, ‘none of this work has yielded convincing conclusions’. Another researcher concluded:

‘the exceptional prebiotic conditions required do not favour asymmetric β-radiolysis as the selector of the exclusive signature of optical activity in living nature.’

Another aspect of parity violation is that the L-amino acids and D-sugars have a theoretically slightly lower energy than their enantiomers so are slightly more stable. But the energy difference is immeasurable—only about 10–17 kT, meaning that there would be only one excess L-enantiomer for every 6×1017 molecules of a racemic mixture of amino acids.

Homochiral template

Some have proposed that a homochiral polymer arose by chance and acted as a template. However, this ran into severe problems. A template of 100 % right-handed poly-C (RNA containing only cytosine monomers) was made (by intelligent chemists!). This could direct the oligomerisation (formation of small chains) of (activated) G (guanine) nucleotides. Indeed, pure right-handed G was oligomerised much more efficiently than pure left-handed G. But racemic G did not oligomerise, because:

‘monomers of opposite handedness to the template are incorporated as chain terminators … This inhibition raises an important problem for many theories of the origin of life.’ (Joyce, G.F., Visser, G.M., van Boeckel, C.A.A., van Boom, J.H., Orgel, L.E. and van Westrenen, J., 1984. Nature, 310:602–4)

Do you like probabilities? Let’s see what Dr. Harold J. Morowitz of Yale University has found on his extensive research for discovering the theoretical limits for the simplest free-living thing which could duplicate itself.

“He took into consideration the minimum operating equipment needed and the space it would require. Also, attention was given to electrical properties and to the hazards of thermal motion. From these important studies, the conclusion is that the smallest such theoretical entity would require 239 or more individual protein molecules.
This is not very much simpler than the smallest actually known autonomous living organism, which is the minuscule, bacteria-like Mycoplasma hominis H39. It has around 600 different kinds of proteins. From present scientific knowledge, there is no reason to believe that anything smaller ever existed. We will, however, use the lesser total of 239 protein molecules from Morowitz’ theoretical minimal cell, which comprise 124 different kinds. 
It was noted earlier that there obviously can be no natural selection if there is no way to duplicate all of the necessary parts. In order to account for the left-handed phenomenon, chance alone, unaided by natural selection, would have to arrange at least one complete set of 239 proteins with all-left-handed amino acids of the universal 20 kinds. There is reason to believe that all 20 of these were in use from the time of life’s origin.
Using figures that were furnished by Morowitz, it can be calculated that the average protein molecule in the theoretical minimal living thing would contain around 445 amino acid units of the usual 20 kinds. One of the 20 types of amino acids, glycine, cannot be left- or right-handed, because its “side chain” is not really a chain, but merely a hydrogen atom like the one opposite it. It can be presumed that this minimal theoretical cell would in many ways resemble bacteria in its make-up. In some bacteria, glycine accounts for just over 8 percent of the total amino acid molecules, so we will estimate that in the average protein of the minimal cell, there will be 35 glycine units in the chain. That will leave 410 of the total 445 which could be either left- or right-handed.

If amino acids had been formed naturally in the “primitive” atmosphere, they would have occurred in statistically equal amounts of the left- and right-handed isomers. This became clear from experiments described in the preceding chapter. That means, then, that if a protein chain is to form by random linkups, all 410 of the nonglycine sites could be occupied with equal ease by either L- or D-type amino acids.
The first one has a 1 out of 2 chance of being left-handed. The same is true for each of the other 409. Since we are now figuring this at equal probability for either hand, the probability at anyone site is not affected by the amino acid before that one in the chain.
To calculate the probability in such a case, the formula to use is the multiplication rule, the heart of probability theory. Mathematician Darrell Huff said it thus: “To find the probability of getting all of several different things, multiply together the chances of getting each one.”
To get the probability of all 410 of the isomeric or handed amino acids of just one protein chain, we must multiply the 1/2 probability which is the case for each position in the chain. It is like flipping a coin 410 times, hoping to get all heads. For each step, there is 1 chance in 2, so we must multiply the 2 by itself (2 x 2 x 2 x . . . x 2). using the figure 410 times. That is 1 chance in 2410. (The exponent means: Multiply together 410 two’s.)
It will be easier to work with this figure if we translate it
to powers of 10 instead of powers of 2. As you know, multiplying 10 by itself is just adding another zero. The equivalent of 2410 is roughly 10123.

The probability that an average-size protein molecule of the smallest theoretically possible living thing would happen to contain only left-handed amino acids is, therefore, 1 in 10123, on the average.
That is a rather discouraging chance. To get the feel of that number, let’s look at it with all the 123 zeros: There is, on the average, 1 chance in –
1,000,000,000,000,000,000,000,000,000,000,000,000,000,
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
that all of the amino acids of a particular protein molecule would be left-handed!” (creationsafaris)

Well, it’s a bit annoying when atheists, materialistic people claim to live completely exempt of faith, after seeing these frightening numbers against them!

“Life on Earth is made of “left-handed amino acids (L-amino acids)”. The question of why organisms on Earth consist of L-amino acids instead of D-amino acids or consist of D-sugar instead of L-sugar is still an unresolved riddle. In other words, a major mystery of life on Earth is that organisms are exclusively made up of left-handed amino acids. Therefore, the effort to solve this problem is one of the biggest in research into the origins of life, a subject that remains enveloped in mystery. “ (PhysOrg)

Sources: 

CMI;

Crev.info

God bless you all!

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