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The Zip Code System Within Cells

A cell, with all its organelles that act in perfect harmony and order within it, has amazing characteristics. Professors at the Swedish Karolinska Institute said that the organization of a cell can be compared to that of a big city such as New York.51

 hücredeki düzen

The structure of the cell
Smooth endoplasmic reticulum
Centrioles
Ribosomes
Smooth
endoplasmic
reticulum
Golgi complex
Nucleolus
Nucleus
Nuclear envelope
Rough endoplasmic reticulum
Lysosome
Nuclear pore
Mitochondrion

When we investigate proteins, which are the building blocks of a cell, we discover some important facts: Every cell contains over a billion or so protein molecules consisting of thousands of different kinds.52In order to get an idea of this huge sum, imagine this example: at the rate of one per second, in order to count a billion proteins, it would take 32 years of continuous and accurate counting. If you take into account your unavoidable need to eat and sleep, your life would probably not be long enough to count the proteins in a single one of your cells. There are about seven billion people in the world, and each person has about 100 trillion cells in his body. Therefore, the number of protein molecules that exist in the world is too great for us to count. Moreover, these proteins are constantly being renewed in every individual; about once every month they disintegrate into the amino acids of which they are composed and are again resynthesized according to the needs of the cells.53 They are reconstituted as a result of the complex operations described by the term "protein synthesis." Some of them are composed as enzymes and are present in nearly every stage of all the complex reactions in the cell; some of them form messenger hormones; some assume special duties in the organization of vital functions, such as carrying oxygen to the blood, stimulating the cells to action and adjusting the level of sugar in the body.

Hücre içindeki trafik

The traffic within cells is much denser than traffic created by human beings. Despite this, in a cell you will never find a traffic jam like the one pictured above. That is because a cell is a perfectly created system.

What we want to concentrate on here is the flow of protein traffic that happens when newly produced proteins change their place in the cell. Because some of these proteins begin to be used immediately within the cell, they must be carried to the place where they are to be used; others are sent to a protein storage area of the cell for later usage. Proteins that will be used outside are removed from the cell under the supervision of the cell membrane. In the meantime, proteins that enter the cell from outside, again under the supervision of the membrane, form an important part of this dense protein traffic. In short, within the tiny parameters of a cell there is an incredible amount of activity. Even rush hour traffic in a large city where millions of people live is really at a standstill compared to the dynamism in a cell. Moreover, this dense activity is carried on by our proteins that are about one millionth of a millimeter in size, that inhabit our cells that are one hundredth of a millimeter in size. It is extraordinary that billions of tiny units of matter fit into a space too small to be seen by the naked eye, and that each one of them is made to run back and forth with great order and harmony to perform their important functions. It is necessary for the continuance of life that this cell traffic flows perfectly. Every protein, either those produced by the factory called a "ribosome" or those that are introduced from other cells have a special place where they will be used. The proteins needed by an organelle, for instance mitochondrion, are different from others. If we consider the organization of a large city, this situation can be compared to the fact that the various production facilities in a city have different needs.

 proteinEndoplasmic reticulum
Synthesized
Protein
Protein packaging
Secretory vesicle
Cell membrane
Protein is released from the cell by
Exocytosis
Ribosome
Carrier vesicle

 

After protein is produced, dense traffic continues within the cell. Protein is either released from the cell by special transporters, carried to the place in the body where it will be used, or left in the golgi apparatus to be stored and packed until it is needed. This is the reason for the constant protein traffic within the cell.

The fact that, within a cell one hundredth of a millimeter in size, a billion proteins are moving at every moment, brings these questions to mind: How do the proteins produced know where they must go? How do they reach the organelles where they are to be used or the target cells outside the cells where they were synthesized without losing their way? How do they come out from inside the membrane that is composed of a fat layer tightly surrounding the organelles? How does this surprisingly dense cell traffic function without an accident?

Let us consider the matter again for a moment substituting a newly born human being for a newly produced protein. Let us give some written and spoken advice to a new baby born in an imaginary city with a billion inhabitants as to where it can find food and clothing, how it can find what it needs, and where it can find a job. Certainly a baby does not know the environment in which it was born; it would not be possible for it to find by itself any place in such a remarkably crowded city. In order for it to find its way without getting lost, it would be necessary for this person to spend years in this city, getting to know it. In order for a person to achieve such a thing he would need a long time; it is certainly surprising, then, that a protein without intelligence or consciousness can do this perfectly.

The secret of how proteins can overcome the obstacles they encounter and find the right address is hidden in the expert design of the cells. Latest research in the science of cells has revealed some wonderful mechanisms in the micro-world of cells.

How is Protein Traffic Within Cells Organized?

Everyone knows that a zip code system is designed to increase the efficiency of communication by getting a letter to the correct address as quickly as possible and with the fewest errors. The really interesting thing is that research has shown that a similar mechanism exists within cells.54It is known that proteins are synthesized by the planned union of hundreds of amino acids. A special section of between 10 and 30 amino acids form a kind of chain that forms the zip code of the protein. In other words, the zip code written on the envelope is composed of numbers and letters, while the zip code in a protein is composed of amino acids. This code is located on one of the ends of the protein or inside it. As a result, every new protein that is synthesized receives instructions as to where it will go inside the cell and how it will go there. Now, let us examine under a highly advanced microscope the journey of a protein within a cell.

Protein sentezi

In order for a letter to reach the right address, it must have a clear address and zip code written on it. In a similar way, every newly produced protein has a special zip code chain that shows it where it will go.

When we look at how a newly synthesized protein, goes to its proper place—for example, endoplasmic reticulum—we see the following: First, the zip code is read by a particle of a molecule called SRP. SRP (Signal Recognition Particle) is a structure especially designed to read the zip code and to help the protein find the channels through which it must pass. It interprets the code in the protein, binds to it and shows it the way like a real guide. Then, the SRP and the protein lock into a protein passage channel and a receptor on the membrane of the endoplasmic reticulum specially designed for them. When the receptor is stimulated in this way, the channel on the membrane is opened. At this stage, the SRP separates from the receptor. All these operations occur with perfect timing and harmony.
At this point, the protein encounters a problem. It is known that proteins are formed when the amino acid chain bends and contorts into a three-dimensional shape. In this situation, it is impossible for protein molecules to pass from the membrane of the endoplasmic reticulum because the passage channel on its membrane is only 0.000000002 meter in diameter. But here we see the existence of a perfect previously designed plan because this problem has already been solved in the production stage. The ribosome that produces the protein produces it in the shape of an uncontorted chain. The structure of this chain makes it possible for the protein to pass through the channel. After the passage is complete, the channel is closed until another passage occurs. The work of the code section in the protein that enters the endoplasmic reticulum comes to an end. For this reason, this section is separated from the protein by particular enzymes; afterwards, the protein folds and takes on its final three dimensional appearance. This situation is like what happens after the letter has reached its destination; the function of the zip code written on the envelope comes to an end. How these enzymes can act consciously and know which of the hundreds, sometimes thousands of amino acids on the protein they will tear off is another wonder. If they tear off any one of the amino acids that make up the protein, other than those that compose the code, the protein may become useless. As we see, at every stage many particles act with consciousness and responsibility. It is a plain fact that this conscious sense of responsibility cannot belong to tiny molecules.
The fact is that the cooperation among the molecules that have a role in these complex functions—proteins, SRP, protein zip codes, ribosomes, receptors, protein channels, enzymes, plasma membranes and other complex functions not touched on here—is flawless. The zip code system in the cell is by itself a great proof of creation. This system that has been used for forty years by human beings has been operating in the trillions of cells in the depths of the bodies of the millions of individuals since the creation of the Prophet Adam (peace be upon him).

The Howard Hughes Medical Institute is known for its research in the field of cellular communication. The president of the Institute, P.W. Choppin, stated that the discovery of the code system in cells is one of the most important discoveries in modern biology. "Günter revealed that each protein has its own 'molecular bar code,' which the cell reads and then guides the protein to the correct location." Choppin has said.55

Proteinin ulaşımı

Some elements in a cell are illustrated in this diagram that shows how proteins are directed by the cell's zip code system. (Chloroplast is an element found only in plant cells.)

The bar code system is not something unfamiliar; we encounter its use frequently in our day-to-day lives. On the back cover of this book you will find an example. Nearly everything in your refrigerator or kitchen cupboards has a bar code on it. In many sectors it is indispensable. This system, which is composed of side-by-side parallel vertical lines, relies on a laser scanner for its interpretation. The laser scanner relays information to a computer and facilitates the performance of a few complicated functions. In brief, the bar code system is a method designed and developed to make our lives easier.
There is no doubt that the bar code has been developed as a result of the special programming and design of the computer and the scanner. This system relies on complex devices, and the harmonious operation of these devices depends on an engineering plan. No one with intelligence and common sense would think otherwise. This being the case, the ideas of those who try to explain such remarkably complex structures as the zip code in the cells (or the bar code system) in terms of chance, display a serious lack of understanding. In the Qur'an, the question is asked, "Or were they created out of nothing, or are they the creators?" (Qur'an, 52: 35), and the impossibility of this is emphasized. The probability that one single protein could be formed by itself (or by chance) is zero, not to mention the billion proteins in one cell. Moreover, because it is impossible that these proteins were formed by chance, it is much more impossible that the coordination, cooperation (and harmony) among them come to be, by chance, in such a way as to enable a body to stay alive for years.

There is no doubt that everything, from atoms to molecules, proteins to cells, has been created by the eternal compassion of God and given to our service. Therefore, it is our duty to think deeply about our Lord's boundless mercy and give thanks to God.

The SRPStructure:The Guide in the Cell

SRP'nin Görevi

Imagine that you are visiting a country for a very short time and that you do not know the language spoken in that country. In this situation, you will urgently need the services of a guide. Similarly, SRP acts as a guide for newly produced proteins.

Imagine that you are making a very short visit to a foreign country whose language you do not know. In this situation you urgently need a guide that will both allow you to communicate with the local people and help you with your visit without getting lost.

Similarly, there is a particle in cells that acts as a guide for newly formed proteins. This guide is the SRP mentioned above whose complex structure is composed of protein and RNS molecules. On the exterior it resembles a bowling pin only 0.000000024 meter in size.

SRP understands the language both of proteins and of the receptor-entrance channel complex on the membrane of the endoplasmic reticulum. The complicated structure of this guide is not yet completely understood; scientists suspect that the RNA molecule in the SRP has an important role, but they have not been able to understand the function of this molecule yet. Moreover, the intricacies of the relation between the SRP guide and the receptor-entrance channel are still unknown.56

SRP Molekülü

The shape of The SRP molecule that guides newly produced proteins resembles a bowling pin.

A professor of molecular biochemistry known for his research in this field, J.A. Doudna, stated that the relation formed between the protein and the RNA, which is one of the components of the SRP, is a "fascinating network"57Indeed, this structure is truly amazing because RNA and protein have been created in such a way as to work in flawless harmony with each other, and have been brought together for the performance of a special function. There is no difference in proposing that this design came to be by chance and maintaining that a cell phone came to be by an alliance made by atoms and molecules among themselves.

The crystal structure of this protein that became understood only in the year 2000 is, without doubt, a product of superior design. It is an eternal sign of the power and knowledge of God.

Communication and Transportation in the Nucleus

Hücre çekirdeği zarındaki geçiş kompleksi

The entrance-exit complexes on the membrane of a cell's nucleus. In the lower section of the illustration you can clearly see the channel opening through which RNA and DNA molecules can pass.

It is known that a cell's nucleus contains a data bank (the DNA molecule) in which all physical characteristics are encoded in their smallest details. Many operations within a cell are carried on with reference to the information in the DNA. Therefore, between the nucleus and the cytoplasm and the various organelles there is heavy protein traffic at every moment. This traffic and communication is organized to respond to the needs of the cell.

The nucleus of the cell is different from other organelles; it is surrounded by a double membrane. On this membrane are located entrance-exit complexes (Nuclear Pore Complexes) used by proteins. These are entrance-exit complexes and not entrance-exit channels because of their structure. Thanks to this special system, comparatively large groups of molecules like RNA and DNA can pass through the nuclear membrane so that the delicate structure of the protein and the molecules are not damaged. When the entrance/exit complex is completely open, they are ten times bigger than the channels in other organelles. Research has shown that there are ten entrances and ten exits every second through each entrance/exit complex.59The entrance and exit of a protein into and out of the nucleus of a cell is completed under the guidance of "karyopherin." This special guide is of various types that bind to the protein and direct it to the entrance/exit complex. Moreover, different proteins and enzymes also have a function in the transfer operation.

This extraordinarily integrated and complex protein transfer system has once again left evolutionist scientists without recourse; Professor Günter Blobel confessed that "the detailed mechanisms for transport across the NPC[Nuclear Pore Complex] are still unknown."60 Take, for example, the karyopherin that establishes communication and directs the passage; the scientific articles written on the functions of this one particle fill thousands of pages. The extraordinary design of one single particle is a clear demonstration of creation. If we notice that several guide particles exist with different characteristics and structures, we better understand that God's eternal knowledge encompasses all things.

Unique Systems Whose Secrets Have Not Yet Been Discovered

Every day scientific research sheds light on the various operations of the cell's "zip code" system. A short time ago, it was understood that a system similar to this existed in the immune system and antibodies are produced by this method. Moreover, it is known that a group of special molecules exist that let blood cells leave the circulatory system and direct them to the relevant tissues.

What we know about the incomparable systems in the cells is quite small compared to what we do not know. The Nobel Prize is usually shared by a number of scientists, but in 1999, only Gunter Blobel took the award for his discovery of the zip code system in cells. In an interview done after he received the award, Professor Blobel said:

We are at the level now that we understand many of the basic mechanisms of protein traffic within the cell but we haven't understood them all yet. We are working, for instance, on traffic between the nucleus and the cytoplasm, and we are far from understanding how this traffic is regulated and how it works.61

The truth is evident. No matter where we go, every point in the depths of space, of the sea, of the forest or in the deep recesses of our bodies is redolent with signs of God's knowledge, art and power. People were unaware in past centuries of the wonders of creation contained in cells; but each one of them captures the imagination today. Every new development in cell biology documents the fact that the claims of evolutionists are deceitful nonsense. At the same time, they show once again that the wonderful order in cells was created by God's single command; "Be" and that they are under His control at each moment. Every detail determined relative to a cell is an occasion for us to exalt the glory and power of our Lord, Almighty God.

His command when He desires a thing is just to say to it, "Be!" and it is. Glory be to Him Who has the Dominion of all things in His Hand. To Him you will be returned. (Qur'an, 36: 82-83)

Dipnotlar

51. The Nobel Foundation, "The Nobel Prize in Physiology or Medicine 1999, Introduction", 1999, http://www.nobel.se/medicine/laureates/1999/illpres/intro.html.

52.Günter Blobel, "Intracellular Protein Traffic", 2000, http://www.hhmi.org/research/investigators/blobel.html.

53.Günter Blobel, "Intracellular Protein Traffic", 2000, http://www.hhmi.org/research/investigators/blobel.html.

54. The Nobel Foundation, "Press Release: The 1999 Nobel Prize in Physiology or Medicine", 1999, http://www.nobel.se/medicine/laureates/1999/press.html.

55. Howard Hughes Medical Institute, "Günter Blobel Wins 1999 Nobel Prize for Physiology or Medicine", 1999, http://www.hhmi.org/news/blobel.html. 

56. R.T. Batey, R.P. Rambo, L. Lucast, B. Rha, J.A. Doudna, "Crystal structure of the ribonucleoprotein core of the signal recognition particle", Science, 18 Şubat 2000, vol.287, no.5456, s.1232-1239.

57. Jennifer A. Doudna, "RNA Catalysis, RNA Processing, and Translation", 2000, http://www.hhmi.org/research/investigators/doudna.html.

58. YALE News Release, "Yale Researcher Identifies Structure of Molecular Zip Code Reader", 2000, http://www.yale.edu/opa/newsr/00-02-17-01.all.html.

59. The Rockefeller University News, "Rockefeller University Cell Biologist, Günter Blobel, Wins 1999 Nobel Prize in Physiology or Medicine", 1999, http://www.rockefeller.edu/pubinfo/blobel.nr.html.

60. E. Conti, M. Uy, L. Leighton, G. Blobel, J. Kuriyan, "Crystallographic Analysis of the Recognition of a Nuclear Localization Signal by the Nuclear Import Factor Karyopherin alpha", Cell, Temmuz 1998, vol.94, s.193-204.

61. Online NewsHour, "Nobel Prize for Medicine", 11 Ekim 1999, http://www.pbs.org/newshour/nobel_1999/blobel.html.

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