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Category Archives: Design

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>

How the flies fly- Video from TED website

From: TED

Michael Dickinson explains how the flies are capable of flying, a very intriguing subject; see the video below, audio in English with subtitles in varied idioms!

 

These annoying insects are an amazing example of biological engineering! They’re capable of some high-speed aeronautic manoeuvres that have long boggled the minds of aircraft designers and engineers. If a male fly chasing a potential mate sees her change course ever so slightly, he will respond with an appropriate change of his own in just 30 milliseconds!

It has long been known that the amazing stability of flies as they zip around has a lot to do with the two tiny club-shaped ‘balancing organs’ they have, called halteres. Some insects have four wings, while others, like the so-called ‘true flies’, have two (hence their ordinal name Diptera).

They have long been known for their function as flight stabilizers, like gyroscopes on airplanes that prevent excessive roll, pitch or yaw. Part of the way this works is that the halteres mostly beat in antiphase to the actual wings. But since such a stabilizing function would tend to make the fly keep flying straight, how does it manage to ‘disable’ this gyroscopic function in order to change course so quickly?

Researcher Dr Michael Dickinson of the University of California at Berkeley, along with a number of colleagues, long knew that flies will perform intricate flight manoeuvres in response to visual stimuli (a fly swatter coming down on them, for instance!). Sophisticated experiments in which flies were tethered in little corsets had shown that images perceived by the fly’s eye-brain system would cause automatic changes in wing activity. Yet a mystery remained, in that for years no one had been able to find evidence of any connecting nerve fibres between the brain and the muscles that controlled the wings.

The breakthrough began when Dickinson was reviewing a much earlier paper that described in great detail some very intricate musculature controlling the halteres. His team then performed more experiments which showed that visual cues while flying did not affect the wing muscles, but significantly affected the muscles controlling the halteres. This suggests that visual information flows directly from the eye/brain to the halteres, not the wings.

Read the full article here: http://creation.com/why-a-fly-can-fly-like-a-fly.

 

God bless you all.

DNA- fascinating video

Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Along with RNA and proteins, DNA is one of the three major macromolecules essential for all known forms of life. Most DNA molecules are double-stranded helices, consisting of two long biopolymers of simpler units called nucleotides—each nucleotide is composed of a nucleobase (guanine, adenine, thymine, and cytosine), recorded using the letters G, A, T, and C, as well as a backbone made of alternating sugars (deoxyribose) and phosphate groups (related to phosphoric acid), with the nucleobases (G, A, T, C) attached to the sugars. DNA is well-suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a built-in duplicate of the encoded information. The following video shows animations of processes which occur within each one of the 10 trillion cells in our body!

Discovery

In 1927, Nikolai Koltsov proposed that inherited traits would be inherited via a “giant hereditary molecule” made up of “two mirror strands that would replicate in a semi-conservative fashion using each strand as a template”. In 1928, Frederick Griffith discovered that traits of the “smooth” form of Pneumococcus could be transferred to the “rough” form of the same bacteria by mixing killed “smooth” bacteria with the live “rough” form. This system provided the first clear suggestion that DNA carries genetic information—the Avery–MacLeod–McCarty experiment—when Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943. DNA’s role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the Hershey–Chase experiment showed that DNA is the genetic material of the T2 phage.

In 1953, James Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal Nature. Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as “Photo 51”) taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases are paired — also obtained through private communications from Erwin Chargaff in the previous years. Chargaff’s rules played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA.

Experimental evidence supporting the Watson and Crick model was published in a series of five articles in the same issue of Nature. Of these, Franklin and Gosling’s paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the Watson and Crick model; this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and in vivo B-DNA X-ray patterns also supported the presence in vivo of the double-helical DNA configurations as proposed by Crick and Watson for their double-helix molecular model of DNA in the previous two pages of Nature.

Repairing system

It’s interesting to notice that the DNA molecule is highly reactive, thus, very unstable… On a good day about one million bases in the DNA in a human cell are damaged. These lesions are caused by a combination of normal chemical activity within the cell and exposure to radiation and toxins coming from environmental sources including cigarette smoke, grilled foods and industrial wastes. So, the organisms have a handful of repairing mechanisms, as said in a recent Science Daily article:

A number of environmental toxins and chemotherapy drugs are alkylation agents that can attack DNA.

When a DNA base becomes alkylated, it forms a lesion that distorts the shape of the molecule enough to prevent successful replication. If the lesion occurs within a gene, the gene may stop functioning. To make matters worse, there are dozens of different types of alkylated DNA bases, each of which has a different effect on replication.

One method to repair such damage that all organisms have evolved is called base excision repair. In BER, special enzymes known as DNA glycosylases travel down the DNA molecule scanning for these lesions. When they encounter one, they break the base pair bond and flip the deformed base out of the DNA double helix. The enzyme contains a specially shaped pocket that holds the deformed base in place while detaching it without damaging the backbone. This leaves a gap (called an “abasic site”) in the DNA that is repaired by another set of enzymes.

Human cells contain a single glycosylase, named AAG, that repairs alkylated bases. It is specialized to detect and delete “ethenoadenine” bases, which have been deformed by combining with highly reactive, oxidized lipids in the body. However, AAG also handles many other forms of akylation damage. Many bacteria, however, have several types of glycosylases that handle different types of damage.

“It’s hard to figure out how glycosylases recognize different types of alkylation damage from studying AAG since it recognizes so many,” says Eichman. “So we have been studying bacterial glycosylases to get additional insights into the detection and repair process.”

That is how they discovered the bacterial glycosylase AlkD with its unique detection and deletion scheme. All the known glycosylases work in basically the same fashion: They flip out the deformed base and hold it in a special pocket while they excise it. AlkD, by contrast, forces both the deformed base and the base it is paired with to flip to the outside of the double helix. This appears to work because the enzyme only operates on deformed bases that have picked up an excess positive charge, making these bases very unstable. If left alone, the deformed base will detach spontaneously. But AlkD speeds up the process by about 100 times. Eichman speculates that the enzyme might also remain at the location and attract additional repair enzymes to the site.

AlkD has a molecular structure that is considerably different from that of other known DNA-binding proteins or enzymes. However, its structure may be similar to that of another class of enzymes called DNA-dependent kinases. These are very large molecules that possess a small active site that plays a role in regulating the cells’ response to DNA damage. AlkD uses several rod-like helical structures called HEAT repeats to grab hold of DNA. Similar structures have been found in the portion of DNA-dependent kinases with no known function, raising the possibility that they play an additional, unrecognized role in DNA repair.

It’s impossible to conceive that such unstable, complex molecule could have originated all alone, by chance and lasted any long in a pre-biotic environment. In a primordial Earth, with a free-oxygen atmosphere, it turns out that it would have no ozon layer, or a very thin one. Thus, the UV light from the Sun would freely bombards the Earth without filtering; the most damaging UV light types would face no barrier, and it’s a fact that UV light damages, degrades polymers!

Many natural and synthetic polymers are attacked by ultra-violet radiation and products made using these materials may crack or disintegrate (if they’re not UV-stable). The problem is known as UV degradation, and is a common problem in products exposed to sunlight. Continuous exposure is a more serious problem than intermittent exposure, since attack is dependent on the extent and degree of exposure.

Effect of UV exposure on polypropylene rope (the left one is damaged, the right one is a new rope)

Add to it the oxidation problem, hydrolysis, etc… Any natural origin of RNA/DNA is inconceivable!

Algae Protein Masters Quantum Mechanics

 

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

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

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

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

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

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

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

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

by Brian Thomas, M.S.

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

 

References

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