Friday, August 24, 2012

Protein Synthesis: The Matchless Production System Recorded in DNA


Proteins are large, complex molecules that perform a great many essential tasks in the body. The proteins that carry out most of the processes in the cell are essential to the formation of the body's tissues and organs and to those organs' ability to do their own jobs. Proteins consist of hundreds or even thousands of smaller units known as amino acids. Twenty different kinds of amino acid are used to give rise to one protein, and every protein consists of a combination of between three hundred and over a thousand amino acids.73 The arrangement of the amino acids determines proteins' unique three-dimensional structures and functions. Thus every organ uses these proteins specially manufactured for it and operates the systems that keep the individual alive.
Inside the human body there are around 200,000 different types of protein, each with its own individual importance. Were the 20 amino acids that comprise proteins to combine together haphazardly, the result would be masses of amino acids in various functionless sequences. Yet these very special arrangements permit proteins to come into existence, essential to human beings' vital functions. Depending on their own particular sequences, proteins are building blocks in the various regions of the body and assume responsibility for different tasks. For example, proteins compose the enzymes that combine to accelerate processes in the body, antibodies that fight disease, and hormones that regulate the functioning of the organs. Each one of these has its own individual, essential importance for the body.
Proteins absorbed in food do not work in the body in their existing form. They are first taken into special laboratories in the cell and broken down into smaller molecules- amino acids. Then, these amino acids are recombined in different sequences to constitute whichever of the 200,000 kinds of proteins encoded in DNA is required at any given time. This mechanism, every stage of which is a miracle in its own right, is known as protein synthesis.

In order for protein synthesis to take place, all the systems within the cell must exist together. If only one component of the whole system is absent, protein cannot be manufactured and therefore, the organism cannot survive. This is just one of the proofs that refute evolutionist claims of chance.

Protein synthesis is the main job of the cells, because proteins carry out just about all the work inside cells. Tens of thousands of different kinds of proteins in the human body are repaired when required and replaced with new ones when they grow old. Blueprints inside the genetic information are noted for the production of a new protein, and the required variety is duly manufactured. The production plan for each protein exists in detailed instructions encoded into DNA.

The molecular biologist Michael Denton refers to the protein production blueprint: Where DNA is the data bank of life, the ultimate repository of all biological information, the proteins are life's animated actors, the universal constructor devices, the nanomanipulators which translate the one-dimensional DNA dream into the vital three-dimensional reality of the cell. By reading and following the instructions in the DNA, the proteins manipulate the atoms and molecules of life into the trillions of unique and specific conformations upon which the miracle of self-replication and self-assembly depends. 74

As an individual goes through daily life, just about all the 100 trillion or so cells in the body are carrying out complex processes at every moment. All cells, apart from reproductive and blood cells, produce around 2,000 proteins a second. The approximately 100 trillion cells in an adult human body flawlessly organize some 150,000,000,000,000,000,000 (150 quintillion) amino acids to give rise to protein chains.75 This process goes on every day, every minute, every second. Prof. Gerald L. Schroeder describes this environment inside the cell:

Our cells are a nonstop marvel. Transport in all directions satisfies the needs for the two thousand proteins manufactured every second of every day, seven days a week. No night-time snooze . . . here.76

The system for the flawless production of proteins, so vitally important to the survival of living things, is incomparably more complex and organized than any Earthly analogy that could be cited. In this complex production plant, there is no room for the slightest error. Any disruption at any stage is immediately put right by the security system, ensuring that the proteins that permit the organism to remain alive are produced with no disruption, at exactly the right time, and in exactly the right place and form.
Another miraculous aspect of protein production is that it occurs at very high speeds. A protein molecule carrying 100 amino acids, for instance, is synthesized by the E. coli bacterium cell in five seconds.77 No factory on Earth is able to complete its entire production process, in a flawless manner, at such a speed. This speed is very important, because several proteins are needed in the cells at any time in order for the organism to survive. In his bookThe Machinery of Life, the molecular biologist David S. Goodsell expresses the importance to life of protein synthesis:
The key molecular process that makes modern life possible is protein synthesis, since proteins are used in nearly every aspect of living. The synthesis of proteins requires a tightly integrated sequence reactions most of which are themselves performed by proteins. Thus posing one of the unanswered riddles of biochemistry: which came first, protein or protein synthesis? If proteins are needed to make proteins, how did the whole thing get started? 78
It is impossible for evolutionists to answer this question, because their Darwinist preconceptions prevent them seeing the facts- or rather, prevents them from openly stating them. The fact is, however, that the fact of creation is inescapable: it is Almighty Allah Who simultaneously creates proteins and the protein synthesis that takes place at great speed inside the cell. Using the coded information in the DNA as a vehicle, our Lord has permitted such vital processes as protein synthesis to continue without interruption.
During protein production, many proteins work at the same time. All the required components work flawlessly together inside the cell. More than 80 ribosome proteins, a messenger molecule with more than 20 amino acids, more than a dozen helper enzymes, more than 100 enzymes that carry out the final processes, and 300 macromolecules, more than 40 of them being RNA molecules- all play co-coordinated roles in protein synthesis.79 A large engineering team would have difficulty co-coordinating this impeccable production system. Yet it takes place in a space no larger than 1/1000 millimeter, and the intense activity of hundreds of much smaller molecules permits life to continue. The absence of just one of the molecules involved in the production will disrupt the entire chain. A system that functions in such a planned way and with such evident consciousness is possible only through creation by Allah, the absolute Lord of all things.
For a detailed account of how protein synthesis actually takes place, see Harun Yahya, The Miracle of Protein, Araştırma Yayıncılık. This chapter will describe only the general lines of the process as we show how use is made of the information in DNA.

1. Transporter RNA (tRNA) Attached inside an RNA molecule
2. Messenger RNA (mRNA)
3. Nucleus Copying Region
A) Whenever the ribosome moves along the mRNA strand, a new amino acid is added to the protein chain. A protein may contain thousands of amino acids.
B) Genes are specially protected inside the cell nucleus. Only copies, in the form of mRNA, are transmitted outside the nucleus.
C) Each amino acid is encoded with the three-base sequence known as the codon. The picture shows glycine, an amino acid.

Synthesizing proteins is the cell's main function, because proteins carry out just about every task inside the cell. For instance, they combine together to constitute enzymes that accelerate the functions within the body, the antibodies that combat disease, and the hormones that regulate the working of internal organs. Each one of these has its own, independent importance for the body.
The tens of thousands of different proteins are manufactured according to the descriptions laid out inside DNA. The fact that DNA can be copied only with the assistance of a number of enzymes within the protein structure -and that production of these enzymes is only possible in the light of the information inside DNA- shows how dependent enzymes and DNA are on one another. Therefore, in order for DNA to be copied, both proteins and DNA need to exist at the same time, right from the outset.
This is clear proof that living things are created in a single moment. Almighty Allah creates both proteins and DNA at one and the same time.
Protein synthesis is carried out in two stages, known as transcription and translation, which permit the information in DNA to be transmitted to RNA, and from there to the proteins.
Transcription, the first step, begins in the cell nucleus. The genetic information in the double strip of DNA is to be transported by means of the single-strip RNA molecule.
Translation, the final step in protein synthesis, takes place in the cell cytoplasm outside the nucleus, where of the genetic information in RNA is transmitted to new proteins.
Let's now look at the general outlines of these stages:
In cells, nucleic acids are found in two separate forms: DNA (short for deoxyribonucleic acid) and RNA (ribonucleic acid), which perform different tasks. The general differences between the two are as follows:

The Wisdom Behind DNA and RNA Molecules Being Different


Their sugars are different:
The backbone of the RNA molecule is ribose sugar, instead of the deoxyribose sugar molecule in DNA.
The bases are different:
There is uracil (U) in RNA instead of the thymine (T) in DNA.
RNA is shorter and consists of just a single strip:
RNA is a polymer (a compound formed by a large number of molecules joining together with chemical bonds in a regular manner). It has a structural similarity to DNA and like DNA, it also carries information. But unlike DNA, RNA consists of a single strip.
DNA is a more stable molecule:
RNA has an extra oxygen atom in every sugar molecule and lacks one carbon atom in every thymine base. The absence of oxygen in DNA's sugar molecules –that is, the fact that DNA has a deoxyribose sugar structure-makes it a more stable molecule than RNA. For that reason, DNA is the ideal molecule for information storage and is far better suited to the long– term storage of data in the cell. Indeed, it is DNA's task to carry information that ensures the survival of the organism and the continuation of subsequent generations. The RNA molecule plays temporary roles and serves in the short-term carrying of information. 80
RNA enters into reactions faster:
In addition, since RNA has an extra hydroxyl (OH) group, it enters into reactions more easily than DNA, but which also makes it less stable. This is why RNA is not as well suited as DNA for storing information. Thanks to the way that the single-strip RNA molecule can adapt to complex three-dimensional structures, it's able to engage in catalytic activities that the strong and double-striped DNA helix cannot perform. (A catalytic effect enables a substance to undergo no change, but to effect in a chemical reaction or the speed at which it does so.) Thanks to their catalytic abilities, RNA molecules can alter chemical structures in a most astonishing manner. For example, during the processes in the cell nucleus, they turn a large copy of the DNA sequence into a "messenger RNA" sequence much smaller than themselves. The ribosome then converts messenger RNA into the protein's amino acid sequence.81
The information in DNA can be reached more easily:
If the RNA molecule had a double-helix structure like that of DNA, the structural folds in RNA would not occur, which would prevent its being recognized by proteins. Also a double-helix structure would give, RNA with a deep recess, making it harder for proteins to reach it and for its coded information to be read.82 Proteins could not recognize a double-helix RNA and its base sequences as easily as they do with DNA. Therefore, DNA is better suited for containing genetic information because it is more stable and more easily reached.83
DNA and RNA are the ideal molecules for their own separate tasks.
RNA carries the genetic message it receives from the DNA inside the nucleus to the cytoplasm (that part of the cell that lies outside the nucleus), where the message is translated. The essential differences between these two molecules help them perform their separate tasks. DNA is a stable and approachable data-preservation center inside the cell, while RNA is a variable carrier that enables genetic information to be translated. In his bookNature's Destiny, the molecular biologist Michael Denton notes the importance of these properties:
... the evidence suggests that any change would be detrimental and no other polymers are known which posses precisely the chemical and physical properties of DNA and RNA.84
RNA Types
RNA, with its single strip, is much more flexible than DNA's double helix. As you see, both the DNA and RNA molecules have been specially created for their own functions. The differences in their structures may seem very minor, but are actually exceedingly important in terms of the jobs they perform, and all these details form a highly complex organization. Prof. Gerald L. Schroeder refers to the complexity in the DNA-RNA mechanism:

One basic cell structure, one basic energy source, one set of organelles common to all life. And one system for regulating this unity, the DNA-RNA team that takes individual lifeless raw materials and organizes them into living, thinking, choosing beings. The complexity in the commonness stretches the imagination. 85 


No human being has any influence on this system. Our Almighty Lord installed this system, too small to be seen with the naked eye, while the individual was still no more than one single cell. Human beings, enfolded by the mercy of Allah, stand in need of Him in all things:

Say: "He is Allah, Absolute Oneness, Allah, the Everlasting Sustainer of all. He has not given birth and was not born. And no one is comparable to Him." (Surat al-Ikhlas, 1-4)

Protein Production According to the Instructions in DNA




Whenever the body needs any kind of protein, a message expressing that need reaches the DNA of the cell where that production is to be performed. There is a very important point here which needs to be borne in mind: when there is a need for any kind of protein in the body it is again certain messenger proteins know where they have to apply, are able to locate those sites in the entire body, and forward the message there in readable form. The protein enabling this communication finds it way without becoming lost in the dark interior of the bloodstream, and deposits its message without any part of it being lost or damaged. In short, we are looking at a considerable awareness and sense of responsibility.
The message reaching the cell nucleus forms the protein as the result of a series of complex and highly organized processes. The way that the demand for protein reaches the correct cells out of all the 100 trillion other cells in the body, how the cells understand what is required of them and immediately goes to work, and produce a perfect result are all phenomena that amaze scientists.
The genetic code in the DNA molecule is so programmed that only the cell itself is capable of knowing its content, its meaning, and how it will affect the body throughout its lifetime. However, these cells are merely masses of unconscious inanimate atoms. Under the direction of our Almighty Lord, Who regulates all things on the Earth and in the skies, processes that human beings are unable to carry out are performed in a perfect manner. In the Qur'an, Allah reveals that:
Hud said,] "I have put my trust in Allah, my Lord and your Lord. There is no creature He does not hold by the forelock. My Lord is on a Straight Path.'  (Surah Hud, 56)
It is Allah Who created the seven heavens and of the Earth the same number, the Command descending down through all of them, so that you might know that Allah has power over all things and that Allah encompasses all things in His knowledge. (Surat at-Talaq, 12)
Protein molecules are produced in blocks, in much the same way that a house is built by bricks placed on top of one another. Every different protein is manufactured according to a specific blueprint. The particular amino acid sequence of each protein is determined according to the data recorded in the DNA. The deciphering of the DNA's genetic code, and protein production based on that information, take place in two main stages:
1- The synthesis of RNA from DNA (transcription)
2- The synthesis of protein from RNA (translation)

. Nucleus
B. Ribosome
C. Cytoplasm
D. Translation
E. Protein
1. rRNA forms from within the DNA chain.
2. mRNA enters the ribosome by passing to the cytoplasm through the pores in the cell membrane.
3. The mRNA attaches to the small sub-unit of the ribosome.
4. Amino acids are brought to the ribosome by tRNA and activated thanks to special enzymes.
5. Weak hydrogen bonds are established between the codons and anti-codons in the ribosome. The amino acids transported are attached by peptide bonds, forming polypeptide.
Twenty kinds of amino acid are used to form one protein. Every protein consists of a combination of 300 to 1,000 amino acids. The production of a new protein takes place according to descriptions in the genetic information.


1- The synthesis of RNA from DNA (transcription):

The first stage in protein production is the synthesis of RNA. This process begins with the opening of the DNA helix. The bases adenine, guanine, cytosine and thymine opposite one another in the DNA molecule combine in such a way as to join the two backbones and give rise to a helical structure. During the transcription phase, these bases let go of one another and the double helix of the DNA molecule begins separating, just like the two sides of a zipper.
As the DNA begins to unravel, a special protein known as RNA polymerase begins reading the DNA by traveling along it. During the course of this reading, new RNA is produced by the successive addition of the corresponding bases. This RNA being manufactured is messenger RNA (mRNA). The difference between mRNA and DNA is that instead of the base adenine being opposite thymine, a base known as uracil (represented by the letter U, for short) does so.
These bases are arranged in groups of three. The messenger RNA, whose production is now complete, is then subjected to a series of processes and separated from the DNA. In much the same way that a sculptor adjusts carved a statue right down to the finest detail, the cell directs a string of enzymes to adjust the crude RNA produced.

2- The synthesis of protein from RNA (translation):

The messenger RNA, whose adjustment processes completed, emerges from the nucleus and bonds an organelle known as the ribosome, the cell's energy-production plant. One feature of the messenger RNA molecule is that its bases are set out in groups of three, known as codons. The reading of these three-part groups begins after mRNA has bonded to the ribosome.
Another variety of RNA known as transporter RNA (Trna) which, during protein synthesis carry the amino acids that will make up the new proteins. Unlike the messenger RNA or DNA molecules, transporter RNA is not long, with only 15 to 20 base sequences. Also, its consecutive bases are bonded in such a way as to form a circle. There are two important regions in the transporter RNA link. The first is the region that permits recognition of the amino acids it will transport; the other region, known as the anti-codon, is consists of three bases that will attach to the mRNA.

Every different protein is produced according to a specific blueprint. Every protein is determined by the amino acid sequence unique to itself and the information recorded in DNA. Protein synthesis takes place in two main stages:
1) The deciphering of the genetic code in the DNA molecule (translation) and
2) The production of protein from the information recorded (transcription). Human beings have no control over this system. By the will of our Almighty Lord, unconscious atoms work together in perfect co-ordination to perform vital functions.


The anti-codon in the transporter RNA attaches to the triple groups known as codons on the mRNA bonded to the ribosome. One after the other, the transporter RNA anti-codons bond to the codons on the messenger RNA and also bring with them amino acids. As the transporter RNAs attach to the codons, the attached amino acids begin bonding to one another. When hundreds or thousands of tRNAs are lined up alongside one another, the amino acids they bear are also lined up side by side and begin protein synthesis by constructing bonds with one another. At that point, the tRNA, whose work is done and that has discharged its load, breaks the bond with the mRNA and separates from the ribosome.

Protein Manufacture According toThe in formation in  The Message is  One of The Proofs of Cretion


1. Large Sub-Unit
2. Small Sub-unit
3. mRNA
4. Amino acid
5. tRNA
6. Anti-Codon
7. Ribosome
8. Second Codon
9. Main Codon
10. Peptide bond
11. Developing protein
12. The ribosome moves right along the mRNA.
13. Departing tRNA
14. Developing Protein
15. Departing Protein
16. Stop Codon
17. Completed Protein
18. Adenine
19. Cytosine
20. Guanine
21. Uracil
A) mRNA works together first with small sub-units of the ribosome, and then with larger ones. The ribosome units are then added on to one another.
B) A particular tRNA carries a particular amino acid.
C) The tRNA anti-codon attaches to the mRNA codon.
D) A subsequent tRNA moves forward, carrying an amino acid, to take up its place on the mRNA.
E) Amino acids are attached by a peptide bond, and the first tRNA departs.
F) The more amino acid is transported by the tRNA, the farther the protein extends.
G) The stop codon halts protein synthesis, and the protein is released.
H) Following protein synthesis, the ribosome units separate.
I) Summary of ribosome movement along the mRNA


A Giant Facility of Miniature Dimensions
The cell contains plant and construction plans for the manufacture of 200,000 types of protein. The functional differences between those proteins are at least as great as those between a plane and a television. From that point of view, there can be no comparison between the production variety in the cell and that in even the most technologically advanced environment.
* The production order is issued
When the body feels the need for any protein, a message expressing that need is sent to the DNA molecule in the nucleus of the cell that will carry out that production.
* The project details for production are received
Once the instruction is received, the first process is the selection and extraction from the DNA of the information concerning the protein needing to be produced.
*The project details are copied
The information concerning structural plan of the protein to be manufactured must be copied onto the messenger RNA (mRNA), once it has been found on the DNA molecule.
*Raw materials are taken to the production center
Once the mRNA bearing the protein data has been installed on the ribosome, the amino acid corresponding to the every code in the mRNA is taken to the ribosome by transfer (tRNA), and the raw materials are bonded to the relevant sites.
 *The project details are translated
Information concerning the protein to be manufactured and the requisite raw materials are now ready. The production order is written in the DNA in a special language. However, the language expressing the production data from the DNA is not one that the amino acids can understand, so the one language must be translated into another.
* Production is completed
The ribosome completes the order demanded of it by the DNA according to the information reaching it.
* Quality control
Several enzymes work on the quality-control process that must take place during the manufacture of a single protein. These enzymes must possess a detailed knowledge of the protein and be aware of every stage of the production process.
* The production delivery is made 
The proteins manufactured inside the cell are transported by very special means to where they will be used, or else stored until the time comes.
This event, here summarized in just a few lines, actually takes place as the result of even more complex intermediate processes. As one goes into greater detail, the miraculous processes seen go far beyond the bounds of human comprehension. How can the tiny cell, consisting of unconscious molecules, feel the need for production? How does it engage in production in the light of requirements? How can molecules composed of carbon, hydrogen, oxygen and nitrogen atoms take precautionary measures? Of course, unconscious molecules themselves do not possess these abilities, but an Almighty Power causes the cell to take these decisions and to work in the light of them. It is Omniscient Allah, the Creator of all living things, Who creates these flawless systems, installs every detail in exactly the right place, and causes them all to work together in complete harmony. 

During production, one single amino acid being added in the wrong place is enough to make a functionless protein molecule. Yet this process is carried out in a flawless manner in all living things. Every tRNA molecule serves as a transporter, carrying every amino acid to the predetermined site and ensuring that there is no impairment in the process. The molecular biologist Michael Denton notes this extraordinary organization:
If each target sequence used to label or address particular regions of the genome were not unambiguously unique, then chaos would inevitably ensure. The genome would resemble a filing cabinet with the same labels on different drawers.86
These actions –requiring immaculate discipline, awareness and responsibility– are a sign that these unconscious molecules have submitted to Omniscient and Almighty Allah and that they behave under His control. In one verse of the Qur'an it is revealed that:
Say: "I seek refuge with the Lord of humanity, the King of humanity, the deity of humanity."  (Surat an-Nas, 1-3)
RNA Polymerase: An Enyzme That Locates A Few Lines From Among Entire Encyclopedias of Data
When a particular protein needs to be manufactured, an enzyme by the name of RNA polymerase goes to the DNA, the cell's data bank, finds the information regarding the protein to be produced, and takes a copy of it. First it must select and extract the relevant letters for the protein to be manufactured from among the 3 billion letters comprising the DNA molecule. The way the polymerase enzyme extracts a few lines of data from those 3 billion letters resembles the instant location of a few lines in an encyclopedia of 1,000 pages with no description being provided.
The data regarding a single protein may sometimes be dispersed in different section of the DNA. For that reason, once the RNA polymerase enzyme has copied the section from where the information begins to where it ends, it will also have copied irrelevant segments. The presence of unnecessary information will lead to the manufacture of useless and unnecessary proteins. At this point, enzymes known as spliceosomes come to the rescue and extract the unnecessary sections from among hundreds of thousands of pieces of information, and then splice the remaining parts together.
Molecules of only a few atoms exhibit miraculous behavior in the RNA-severing process. They correct gaps and errors in the text, just like an editor. These atoms know which protein the RNA polymerase wants to manufacture, are able to differentiate between information necessary for that protein to come into being and needless information, and they carry out this task among hundreds of thousands of pieces of data without making a single error. They also realize immediately when their presence is required, and arrive to begin work without a moment's delay.
In order to read the information contained in human DNA, hundreds of leading scientists managed to do this only within the framework of the Human Genome Project, working for some 10 years with the most highly developed technology. They have still been unable to establish which letters are used for the manufacture of which protein. In contrast, trillions of RNA polymerase enzymes in the body's 100 trillion cells are constantly reading the information contained in DNA from beginning to end and extracting and providing the information requested in a flawless and immaculate manner. This extraordinary phenomenon is one clear proof that Almighty Allah, the Creator of all things, creates the RNA polymerase and bestows this ability upon it.





























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