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The interdependent and irreducible structures required to make proteins

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The interdependent and irreducible structures required to make proteins

http://reasonandscience.heavenforum.org/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins

To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors, which require the very own processing procedure described below, which makes its origin an irreducible  catch22 problem: 

THE GENE REGULATORY NETWORK "SELECTS" WHEN, WHICH GENE IS TO BE EXPRESSED
INITIATION OF TRANSCRIPTION BY RNA POLYMERASE
TRANSCRIPTION ERROR CHECKING BY CORE POLYMERASE AND TRANSCRIPTION FACTORS
RNA CAPPING
ELONGATION
SPLICING
CLEAVAGE
POLYADENYLATION AND TERMINATION
EXPORT FROM THE NUCLEUS TO THE CYTOSOL
INITIATION OF PROTEIN SYNTHESIS (TRANSLATION) IN THE RIBOSOME
COMPLETION OF PROTEIN SYNTHESIS  
PROTEIN FOLDING
MATURATION
RIBOSOME QUALITY CONTROL
PROTEIN TARGETING TO THE RIGHT CELLULAR COMPARTMENT
ENGAGING THE TARGETING MACHINERY BY THE PROTEIN SIGNAL SEQUENCE
CALL CARGO PROTEINS TO LOAD/UNLOAD THE PROTEINS TO BE TRANSPORTED
ASSEMBLY/DISASSEMBLY OF THE TRANSLOCATION MACHINERY
VARIOS CHECKPOINTS FOR QUALITY CONTROL AND REJECTION OF INCORRECT CARGOS
TRANSLOCATION TO THE ENDOPLASMIC RETICULUM
POSTRANSLATIONAL PROCESS OF PROTEINS IN THE ENDOPLASMIC RETICULUM OF TRANSMEMBRANE PROTEINS AND WATER-SOLUBLE PROTEINS
GLYCOSILATION OF MEMBRANE PROTEINS IN THE ER ( ENDOPLASMIC RETICULUM )
ADDITION OF OLIGOSACCHARIDES
INCORRECTLY FOLDED PROTEINS ARE EXPORTED FROM THE ER, AND DEGRADED IN THE CYTOSOL
TRANSPORT OF THE PROTEIN CARGO TO THE END DESTINATIONS AND ASSEMBLY

Paul Davies, the origin of life, page 59
Proteins are a godsend to DNA because they can be used both as building material, to make things like cell walls, and as enzymes, to supervise and accelerate chemical reactions. Enzymes are chemical catalysts that ‘oil the wheels’ of the biological machine. Without them metabolism would grind to a halt, and there would be no energy available for the business of life. Not surprisingly, therefore, a large part of the DNA databank is used for storing instructions on how to make proteins. Here is how those instructions get implemented. Remember that proteins are long chain molecules made from lots of amino acids strung together to form polypeptides. Each different sequence of amino acids yields a different protein. The DNA has a wish list of all the proteins the organism needs. This information is stored by recording the particular amino acid sequence that specifies each and every protein on the list. It does so using DNA's four-letter alphabet A, G, C and T; the exact sequence of letters spells out the amino acid recipe, protein by protein – typically a few hundred base pairs for each. To turn this dry list of amino acids into assembled, functioning proteins, DNA enlists the help of a closely related molecule known as RNA (for ribonucleic acid). RNA is also made from four bases, A, G, C and U. Here U stands for uracil; it is similar to T and serves the same purpose alphabetically. RNA comes in several varieties; the one of interest to us here is known as messenger RNA, or mRNA for short. Its job is to read off the protein recipes from DNA and convey them to tiny factories in the cell where the proteins are made. These mini-factories are called ribosomes, and are complicated machines built from RNA and proteins of various sorts. Ribosomes come with a slot into which the mRNA feeds, after the fashion of a punched tape of the sort used by old-fashioned computers.

The mRNA ‘tape’ chugs throughthe ribosome, which then carries out its instructions bit by bit, hooking amino acids together, one by one in the specified sequence, until an entire protein has been constructed. Earthlife makes proteins from 20 different varieties of amino acids, 2 and the mRNA records which one comes after which so the ribosome can put them together in the right order. It is quite fascinating to see how the ribosome goes about joining the amino acids up into a chain. Naturally the amino acids don't obligingly come along in the right order, ready to be hooked on to the end of the chain. So how does the ribosome ensure that the mRNA gets its specified amino acid at each step? The answer lies with another set of RNA molecules, called transfer RNA, or tRNA for short. Each particular tRNA molecule brings along to the ribosome factory one and only one sort of amino acid stuck to its end, to present it to the production line. At each step in the assembly of the protein, the trick is to get the right tRNA, with the right amino acid attached, to give up its cargo and transfer it to the end of the growing protein chain, while rejecting any of the remaining 19 alternatives that may be on offer. This is accomplished as follows. The mRNA (remember, this carries the instructions) exposes a bit of information (i.e. a set of ‘letters’) that says ‘add amino acid such-and-such now’. The instructions are implemented correctly because only the targeted tRNA molecule, carrying the designated amino acid, will recognize the exposed bit of mRNA from its shape and chemical properties, and bind to it. The other tRNA molecules the ones that are carrying the ‘wrong’ amino acids – won't fit properly into the binding site. Having thus seduced the right tRNA molecule to berth at the production line, the next step is for the ribosome to persuade the newly arrived amino acid cargo to attach itself to the end of the protein chain. The chain is waiting in the ribosome, dangling from the end of the previously selected tRNA molecule.

At this point the latter molecule lets go and quits the ribosome, passing the entire chain on to the newly arrived tRNA, where it links on to the amino acid it has brought with it. The chain thus grows by adding amino acids to the head rather than the tail. If you didn't follow all of this on the first read through, don't worry, it isn't essential for understanding what follows. I just thought it was sufficiently amazing to be worth relating in some detail. When the protein synthesis is complete, the ribosome receives a ‘stop’ signal from the mRNA ‘tape’ and the chain cuts loose. The protein is now assembled, but it doesn't remain strung out like a snake. Instead it rolls up into a knobbly ball, rather like a piece of elastic that's stretched and allowed to snap back. This folding process may take some seconds, and it is still something of a mystery as to how the protein attains the appropriate final shape. To work properly, the three-dimensional form of the protein has to be correct, with the bumps and cavities in all the right places, and the right atoms facing outwards. Ultimately it is the particular amino acid sequence along the chain that determines the final threedimensional conformation, and therefore the physical and chemical properties, of the protein. This whole remarkable sequence of events is repeated in thousands of ribosomes scattered throughout the cell, producing tens of thousands of different proteins. It is worth repeating that, in spite of the appearance of purpose, the participating molecules are completely mindless. Collectively they may display systematic cooperation, as if to a plan, but individually they just career about. The molecular traffic within the cell is essentially chaotic, driven by chemical attraction and repulsion and continually agitated by thermal energy. Yet out of this blind chaos order emerges spontaneously.



Can an alphabet arise without an intelligent mind inventing it? What good is an alphabet for, if there is no medium like ink and paper to write a message on the paper,  if there is no one to actually write a message  and no one to read and understand it upon common agreement of meaning of words and language, between sender and receiver ??

Can the DNA code arise without an intelligent mind inventing it? What good is the DNA code for, if there is no medium like the DNA double helix, to encode the information required to make proteins? What good is the DNA code for, the software, and the DNA double helix, the hardware, if there is no machinery to read, transcribe and translate the message stored in DNA to make proteins? Must not all come into existence all at ones, otherwise, if one is missing, the others have no function?

http://www.ncbi.nlm.nih.gov/pubmed/8335231
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, a collection of punctuation marks and regulatory sites, semantics.

In the cell, things are however far more complex. There is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to make the final product, that is proteins. That chain is constituted by INITIATION OF TRANSCRIPTION, CAPPING,  ELONGATION,  SPLICING, CLEAVAGE, POLYADENYLATION, AND TERMINATION, EXPORT FROM THE NUCLEUS TO THE CYTOSOL, INITIATION OF PROTEIN SYNTHESIS (TRANSLATION), COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING. In order for evolution to work, the robot-like working machinery and assembly line must be in place, fully operational. So the origin of the machines cannot be explained through evolution. All it is left, are random chemical reactions, or design. Choose which explanation seems more fitting the evidence.








Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. 4

The Signal recognition particle (SRP) and its receptor comprise a universally conserved and essential cellular machinery that couples the synthesis of nascent proteins to their proper membrane localization.  The SRP and SRP receptor interacts with the cargo protein and the target membrane in this fundamental cellular pathway

Proper localization of proteins to their correct cellular destinations is essential for sustaining the order and organization in all cells. Roughly 30% of the proteome is initially destined for the eukaryotic endoplasmic reticulum (ER), or the bacterial plasma membrane. The majority of these proteins are delivered by the Signal Recognition Particle (SRP), a universally conserved protein targeting machine (14). 

The cotranslational SRP pathway minimizes the aggregation or misfolding of nascent proteins before they arrive at their cellular destination, and is therefore highly advantageous in the targeted delivery of membrane and secretory proteins. Despite the divergence of targeting machinery, the SRP pathway illustrates several key features that are general to almost all protein targeting processes: 

(i) the cellular destination of a protein is dictated by its ‘signal sequence’, which allows it to engage a specific targeting machinery; 
(ii) targeting factors cycle between the cytosol and membrane, acting catalytically to bring cargo proteins to translocation sites at the target membrane; and 
(iii) targeting requires the accurate coordination of multiple dynamic events including cargo loading/unloading, targeting complex assembly/disassembly, and the productive handover of cargo from the targeting to translocation machinery. 

Question : How could and would the protein find its way to the right destination without the signal sequence just right, right from the beginning ? 

Not surprisingly, such molecular choreography requires energy input, which is often harnessed by GTPase or ATPase modules in the targeting machinery. 

Cargo Recognition by the SRP

Timely recognition of signal sequences by the SRP is essential for proper initiation of cotranslational protein targeting. Signal sequences that engage the SRP are characterized, in general, by a core of 8–12 hydrophobic amino acids. 

The multiple conformational rearrangements in the SRP•FtsY GTPase complex provide a series of additional checkpoints to further reject the incorrect cargos. These include: 

(i) formation of the early intermediate, which is stabilized over 100-fold by the correct, but not incorrect cargos (Figure 3B, red arrow b); 
(ii) rearrangement of the early intermediate to the closed complex, which is ~10-fold faster with the correct than the incorrect cargos (Figure 3B, red arrow c); and 
(iii) GTP hydrolysis by the SRP•FtsY complex, which is delayed ~8-fold by the correct cargo to give the targeting complex a sufficient time window to identify the membrane translocon.

In contrast, GTP hydrolysis remains rapid with the incorrect cargo (t1/2 < 1s), which could abort the targeting of incorrect cargos (Figure 3B, arrow d). A mathematical simulation based on the kinetic and thermodynamic parameters of each step strongly suggest that all these fidelity checkpoints are required to reproduce the experimentally observed pattern of substrate selection by the SRP (40).

These results support a novel model in which the fidelity of protein targeting by the SRP is achieved through the cumulative effect of multiple checkpoints, by using a combination of mechanisms including 

cargo binding, induced SRP–SR assembly, and kinetic proofreading through GTP hydrolysis.  Additional discrimination could be provided by the SecYEG machinery, which further rejects the incorrect cargos (102).  Analogous principles have been demonstrated in the DNA and RNA polymerases (103104), the spliceosome (105), tRNA synthetases (106) and tRNA selection by the ribosome (107), and may represent a general principle for complex biological pathways that need to distinguish between the correct and incorrect substrates based on minor differences.

The crowded ribosome exit site

Accumulating data now indicate that the ribosome exit site is a crowded environment where multiple protein biogenesis factors interact. As a newly synthesized protein emerges from the ribosomal exit tunnel, it interacts with a host of cellular factors that facilitate its folding, localization, maturation, and quality control. These include molecular chaperones.

Many proteins need to enter the ER for modification with sugars this occurs at the same time that they are being synthesized by the ribosome translation begins with synthesis of a short signal peptide sequence a signal recognition particle a protein complexbinds to the signal peptide while translation continues the SRP then binds to its receptor in the ER membrane anchoring the ribosome the ribosome binds its receptor and the signal peptide meets the protein translocator translation proceeds and the protein passes through the translocator the signal peptidase cleaves the signal peptide leaving the new protein molecule in the lumen of the endoplasmic reticulum

A non-mechanical example of irreducible complexity can be seen in the system that targets proteins for delivery to subcellular compartments. In order to find their way to the compartments where they are needed to perform specialized tasks, certain proteins contain a special amino acid sequence near the beginning called a 'signal sequence.'' As the proteins are being synthesized by ribosomes, a complex molecular assemblage called the signal recognition particle or SRP, binds to the signal sequence. This causes synthesis of the protein to halt temporarily. During the pause in protein synthesis the SRP is bound by the transmembrane SRP receptor, which causes protein synthesis to resume and which allows passage of the protein into the interior of the endoplasmic reticulum (ER). As the protein passes into the ER the signal sequence is cut off. For many proteins the ER is just a way station on their travels to their final destinations (Figure 10.3). 



Proteins which will end up in a lysosome are enzymatically ``tagged'' with a carbohydrate residue called mannose- 6-phosphate while still in the ER. An area of the ER membrane then begins to concentrate several proteins; one protein, clathrin, forms a sort of geodesic dome called a coated vesicle which buds off from the ER. In the dome there is also a receptor protein which binds to both the clathrin and to the mannose-6-phosphate group of the protein which is being transported. The coated vesicle then leaves the ER, travels through the cytoplasm, and binds to the lysosome through another specific receptor protein. Finally, in a maneuver involving several more proteins, the vesicle fuses with the lysosome and the protein arrives at its destination. During its travels our protein interacted with dozens of macromolecules to achieve one purpose: its arrival in the lysosome. 

Virtually all components of the transport system are necessary for the system to operate, and therefore the system is irreducible. And since all of the components of the system are comprised of single or several molecules, there
are no black boxes to invoke. The consequences of even a single gap in the transport chain can be seen in the hereditary defect known as Icell disease. It results from a deficiency of the enzyme that places the mannose-6-phosphate on proteins to be targeted to the lysosomes. I-cell disease is characterized by progressive retardation, skeletal deformities, and early death.

Transport by vesicles: when proteins are made on the rough endoplasmic reticulum (RER), they get loaded into the Golgi apparatus. They are then sorted, modified and packaged in vesicles made from the budding-off of the Golgi membrane and discharged.
Sorting signals directs the protein to the organelle. The signal is usually a stretch of amino acid sequence of about 15-60 amino acids long.
There are at least three principles that characterize all vesicles mediated transport within cells:

i. The formation of membrane vesicles from a larger membrane occurs through the assistance of a protein coat such as clathrin that engulfs the protein because an adapter protein such as adaptin binds both to the coat and to the cargo protein bringing both close together. 5
The adaptin traps the cargo protein by biding with it’s receptors. After assembly particles bind to the clathrin protein they assemble into a basket-like network on the cytosolic surface of the membrane to shape it into a vesicle. Their final budding-off requires a GTP-binding protein called dynamin.
ii. The process is facilitated by a number of GTP-binding proteins (ex; dynamin) that assemble a ring around the neck of a vesicle and through the hydrolysis of the phosphate group of GTP to GDP until the vesicle pinches off. In other words, GTP is one of the main sources of cellular energy for vesicle movement and fusion.
iii. After a transport vesicle buds-off from the membrane, it is actively transported by motor proteins that move along cytoskeleton fibers to its destination. The vesicle then fuses with a target membrane and unloads the cargo (protein). But in order to fuse a vesicle with the membrane of another compartment, they both require complementary proteins, which in this case is soluble N-ethylmalei mide-sensitive-factor attachment protein receptor or, ahem, SNARE present in the membrane – one for the vesicle (vesicular SNARE) and one for the target membrane (t-SNARE).



http://reasonandscience.heavenforum.org/t2039-interdependence-of-the-dna-double-helix-the-genetic-code-and-the-machinery-to-transcribe-and-translate-the-code-to-make-proteins#3464



Last edited by Admin on Sat Dec 23, 2017 8:43 am; edited 12 times in total

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what reason are there to be transit signals, if there is no transit, no cars, no one to actually read the signal and act upon its instructions, and either passing the cross road, or stop upon the red light?

Same with genetic instructions : A TATA box is a DNA sequence that indicates where a genetic sequence can begin to be readed and transcribed. What would it be good for, and for what reason arise, if there would not be the sophisticated molecular machine complexes to read the sequence through transcription factors, no  TATA-binding proteins to bind to the promoter sequence, and no RNA polymerase enzymes to actually start transcription ? promoter regions in genes have no other functions. They are interdependent.

http://reasonandscience.heavenforum.org/t2039-interdependence-of-the-dna-double-helix-the-genetic-code-and-the-machinery-to-transcribe-and-translate-the-code-to-make-proteins#3465

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3 On protein synthesis on Sat Sep 05, 2015 6:55 pm

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