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Translation through ribosomes, amazing nano machines

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Ribosomes amazing nano machines

http://reasonandscience.heavenforum.org/t1661-translation-through-ribosomes-amazing-nano-machines

* Each cell contains around 10 million ribosomes, i.e. 7000 ribosomes are produced in the nucleolus each minute.
*Each ribosome contains around 80 proteins, i.e. more than 0.5 million ribosomal proteins are synthesised in the cytoplasm per minute.
*The nuclear membrane contains approximately 5000 pores. Thus, more than 100 ribosomal proteins are imported from the cytoplasm to the nucleus per pore and minute. At the same time 3 ribosomal subunits are exported from the nucleus to the cytoplasm per pore and minute.

The evidence from the ribosome
a. “Spontaneous formation of the unlocked state of the ribosome is a multi-step process.”
b. The L1 stalks of the ribosome bend, rotate and uncouple – undergoing at least four distinct stalk positions while each tRNA ratchets through the assembly tunnel.  At one stage, for instance, “the L1 stalk domain closes and the 30S subunit undergoes a counterclockwise, ratchet-like rotation” with respect to another domain of the factory.  This is not simple.  “Subunit ratcheting is a complex set of motions that entails the remodeling of numerous bridging contacts found at the subunit interface that are involved in substrate positioning.”
c.The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is “shocking” and reveals just how much of a stickler (insisting) the ribosome is about high-fidelity protein synthesis. (Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics: The Ribosome: Perfectionist Protein-maker Trashes Errors, 2009)
4. Interactions between molecules are not simply matters of matching electrons with protons.  Instead, large structural molecules form machines with moving parts.  These parts experience the same kinds of forces and motions that we experience at the macro level: stretching, bending, leverage, spring tension, ratcheting, rotation and translocation.  The same units of force and energy are appropriate for both – except at vastly different levels.
5. Every day, essays about molecular machines are giving more and more biomolecular details, many without mentioning evolution and giving details about the process how these machines evolved.
6. These complexities are the work of God.
7. Hence God exists.


Comparative genomic reconstructions of the gene repertoire of LUCA(S) point to a complex translation system that includes at least 18 of the 20 aminoacyl-tRNA synthetases (aaRS), several translation factors, at least 40 ribosomal proteins, and several enzymes involved in rRNA and tRNA modification. It appears that the core of the translation system was already fully shaped in LUCA(S) (Anantharaman, et al., 2002). 






animation:

http://telstar.ote.cmu.edu/biology/animation/ProteinSynthesis/proteinsynthesis.html

The RNA Message Is Decoded in Ribosomes

The synthesis of proteins is guided by information carried by mRNA molecules. To maintain the correct reading frame and to ensure accuracy (about 1 mistake every 10,000 amino acids), protein synthesis is performed in the ribosome, a complex catalytic machine made from more than 50 different proteins (the ribosomal proteins) and several RNA molecules, the ribosomal RNAs (rRNAs). A typical eukaryotic cell contains millions of ribosomes in its cytoplasm



The large and small ribosome subunits are assembled at the nucleolus, where newly transcribed and modified rRNAs associate with the ribosomal proteins that have been transported into the nucleus after their synthesis in the cytoplasm. These two ribosomal subunits are then exported to the cytoplasm, where they join together to synthesize proteins. Eukaryotic and bacterial ribosomes have similar structures and functions, being composed of one large and one small subunit that fit together to form a complete ribosome with a mass of several million daltons



There are millions of protein factories in every cell. Surprise, they’re not all the same 2

The plant that built your computer isn't churning out cars and toys as well. But many researchers think cells' crucial protein factories, organelles known as ribosomes, are interchangeable, each one able to make any of the body's proteins. Now, a provocative study suggests that some ribosomes, like modern factories, specialize in manufacturing only certain products. Such tailored ribosomes could provide a cell with another way to control which proteins it generates. They could also help explain the puzzling symptoms of certain diseases, which might arise when particular ribosomes are defective.

Biologists have long debated whether ribosomes specialize, and some remain unconvinced by the new work. But other researchers say they are sold on the finding, which relied on sophisticated analytical techniques. "This is really an important step in redefining how we think about this central player in molecular biology," says Jonathan Dinman, a molecular biologist at the University of Maryland in College Park.

A mammalian cell may harbor as many as 10 million ribosomes, and it can devote up to 60% of its energy to constructing them from RNA and 80 different types of proteins. Although ribosomes are costly, they are essential for translating the genetic code, carried in messenger RNA (mRNA) molecules, into all the proteins the cell needs. "Life evolved around the ribosome," Dinman says.

The standard view has been that a ribosome doesn't play favorites with mRNAs—and therefore can synthesize every protein variety. But for decades, some researchers have reported hints of customized ribosomes. For example, molecular and developmental biologist Maria Barna of Stanford University in Palo Alto, California, and colleagues reported in 2011 that mice with too little of one ribosome protein have short tails, sprout extra ribs, and display other anatomical defects. That pattern of abnormalities suggested that the protein shortage had crippled ribosomes specialized for manufacturing proteins key to embryonic development.

Definitive evidence for such differences has been elusive, however. "It's been a really hard field to make progress in," says structural and systems biologist Jamie Cate of the University of California (UC), Berkeley. For one thing, he says, measuring the concentrations of proteins in naturally occurring ribosomes has been difficult.

In their latest study, published online last week in Molecular Cell, Barna and her team determined the abundances of various ribosome proteins with a method known as selected reaction monitoring, which depends on a type of mass spectrometry, a technique for sorting molecules by their weight. When the researchers analyzed 15 ribosomal proteins in mouse embryonic stem cells, they found that nine of the proteins were equally common in all ribosomes. However, four were absent from 30% to 40% of the organelles, suggesting that those ribosomes were distinctive. Among 76 ribosome proteins the scientists measured with another mass spectrometry-based method, seven varied enough to indicate ribosome specialization.

Barna and colleagues then asked whether they could identify the proteins that the seemingly distinctive ribosomes made. A technique called ribosome profiling enabled them to pinpoint which mRNAs the organelles were reading—and thus determine their end products. The specialized ribosomes often concentrated on proteins that worked together to perform particular tasks. One type of ribosome built several proteins that control growth, for example. A second type churned out all the proteins that allow cells to use vitamin B12, an essential molecule for metabolism. That each ribosome focused on proteins crucial for a certain function took the team by surprise, Barna says. "I don't think any of us would have expected this."

Ribosome specialization could explain the symptoms of several rare diseases, known as ribosomopathies, in which the organelles are defective. In Diamond-Blackfan anemia, for instance, the bone marrow that generates new blood cells is faulty, but patients also often have birth defects such as a small head and misshapen or missing thumbs. These seemingly unconnected abnormalities might have a single cause, the researchers suggest, if the cells that spawn these different parts of the body during embryonic development carry the same specialized ribosomes.

Normal cells might be able to dial protein production up or down by adjusting the numbers of these specialized factories, providing "a new layer of control of gene expression," Barna says. Why cells need another mechanism for controlling gene activity isn't clear, says Cate, but it could help keep cells stable if their environment changes.

1. from the book: The Logic of Chance: The Nature and Origin of Biological Evolution , page 228, By Eugene V. Koonin
2. http://www.sciencemag.org/news/2017/06/there-are-millions-protein-factories-every-cell-surprise-they-re-not-all-same
3. http://www.nobelprize.org/educational/medicine/dna/a/translation/ribosome_ass.html



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keggs pathway


http://iaincarstairs.wordpress.com/2011/12/26/more-non-random-dna-wonders/

Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name!



The Ribosome: Perfectionist Protein-Maker Trashes Error

http://reasonandscience.heavenforum.org/t1661-ribosomes-amazing-nano-machines


http://iaincarstairs.wordpress.com/2013/03/25/as-smart-as-molecules/

One machine common to all life on Earth is the ribosome.  Its strongly conserved nature, and the common sense observation that it makes everything else, indicates its central position in evolution.  The ribosome is not a single tool but a workshop split into two major parts, all created (using E. coli as an example) from around 7,400 amino acids, and around 250,000 atoms, all primed to use the strongest possible codon-amino acid mapping out of a practically endless range of possibilities.

Ribosomes can be so numerous as to make up 25% of the cell mass of E. coli. A striking feature of the ribosome is that, even given the large assorted collection of subunits, it self-assembles in vitro!

The core of the ribosome is RNA, supporting the idea that early forms of life relied on RNA rather than DNA.  But if such a workshop is necessary to create proteins, whether from templates of RNA or DNA – from where could the ribosome come from?  More vexing still for Darwinism is how editorial precision could arise in a system in which errors themselves were the key to prolific reproductive success at the start.  Why change a winning hand?

New discoveries are being made about the ribosome all the time.  Relevant to Darwinism, in 2009 Nature published some new discoveries by Johns Hopkins researchers concerning the remarkable actions of the ribosome’s ruthless quality control editor; if you think I tend to anthropomorphise molecules, note how the researchers detail -

   ..a new “proofreading step” during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a “delete” button.

   It turns out.. ..that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

   “What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story,” says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. “There’s no second chance.”

   “We thought that once the mistake was made, it would have just gone on to make the next bond and the next,” Green says. “But instead, we noticed that one mistake on the ribosomal assembly line begets another, and it’s this compounding of errors that leads to the partially finished protein being tossed into the cellular trash.”

   To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction Green says is “shocking” and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.

   http://phys.org/news150559493.html#jCp




The translation process in the ribosome to occur, the ribosome must be able to proceed and go through the full translation sequence, it must be fully functional, no intermediate evolutionary stage will do it : beside this, it consists of two main subunits, ( beside a significant number of co-factors , which help in the build up process of the ribosome ) which makes it a irreducible complex system.

Replication most probably would not occur at pre-stage of a common ancestor, so evolution cannot be proposed as a driving factor at this stage.

lifeorigin::
RNA replication in the lab makes use of extensive investigator interference. Chemicals like amino acids, aldehydes, and sugars (other than ribose) are arbitrarily excluded. Very specific activation agents are used to encourage replication (ImpA for adenine, ImpG for guanine, ImpC for cytosine, and ImpU for uracil). The concentration of the chemicals (especially cytosine and ribose) is billions and billions of orders of magnitude higher than what one would expect under plausible prebiotic conditions.

Shajani Z :
Ribosome assembly needs the contributions of several assembly cofactors , including Era, RbfA, RimJ, RimM, RimP, and RsgA, which associate with the 30S subunit, and CsdA, DbpA, Der, and SrmB, which associate with the 50S subunit. These subunits would have no function of their own, why then would random processes produce them without a final goal and no forsight of function ?
Five following conditions would all have to be met in the biosynthesis process of the Ribosome:
Kairosfocus
C1: Availability. Among the parts available for recruitment to form a biological system consisting of multiple parts, there would need to be ones capable of performing the highly specialized tasks of the specific system, even though all of the items serve some other function or no function in another system where they were recruited from.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination.The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits  are put together in the right order, they also need to interface correctly.

The parts must be coordinated in just the right way: even if all of the parts of a ribosome are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits are put together in the right order, they also need to interface correctly.

Resumed : For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or /  and evolution,  since we observe all the time minds capabilities producing  machines and factories, producing machines and end products.



http://www.hopkinsmedicine.org/news/media/releases/Lost_In_Translation

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist

Johns Hopkins researchers, reporting in the journal Nature January 7, have discovered a new "proofreading step" during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a "delete" button.

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.

To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. "The cell is a wasteful system in that it makes something and then says, forget it, throw it out,"

That looks all ingeniously designed.......

http://www.nytimes.com/2009/10/08/science/08nobel.html?_r=0
Besides the implications for biomedical research, another consequence of the ribosome work was to resolve an old “classic chicken and egg problem” , Dr. Berg of the National Institute of General Medical Sciences explained. If ribosomes are needed to make proteins but they are also made of proteins, which came first?

J.Sarfati :
the DNA information requires a complex decoding machine, the ribosome, but the instructions to build ribosomes are on the DNA. And decoding requires energy from ATP, built by ATP-synthase motors, built from instructions in the DNA decoded by ribosomes … “vicious circles” for any materialistic origin theory, as leading philosopher of science Karl Popper put it .

http://newswire.rockefeller.edu/2013/08/14/structural-biologist-interested-in-ribosome-assembly-to-join-rockefeller-faculty/
What’s more, it’s something of a chicken-and-egg problem. “You need the machinery to be in place in order to manufacture proteins, but the machinery itself is made of proteins that must be manufactured,” Klinge says.

well, as far as i know without ribosomes there is no protein synthesis, without protein synthesis there is no life, without life there is no evolution so ribosomes cant come to existence via evolution so how did the form?

Facing these facts, i believe theists are justified to hold the position, that design explains best the origin of Ribosomes, and the origin of life.



well, as far as i know without ribosomes there is no protein synthesis, without protein synthesis there is no life, without life there is no evolution so ribosomes cant come to existence via evolution so how did the form?

The translation process in the ribosome to occur, the ribosome must be able to proceed and go through the full translation sequence, it must be fully functional, no intermediate evolutionary stage will do it : beside this, it consists of two main subunits, ( beside a significant number of co-factors , which help in the build up process of the ribosome ) which makes it a irreducible complex system.

Replication most probably would not occur at pre-stage of a common ancestor, so evolution cannot be proposed as a driving factor at this stage.

lifeorigin::
RNA replication in the lab makes use of extensive investigator interference. Chemicals like amino acids, aldehydes, and sugars (other than ribose) are arbitrarily excluded. Very specific activation agents are used to encourage replication (ImpA for adenine, ImpG for guanine, ImpC for cytosine, and ImpU for uracil). The concentration of the chemicals (especially cytosine and ribose) is billions and billions of orders of magnitude higher than what one would expect under plausible prebiotic conditions.

Shajani Z :Ribosome assembly needs the contributions of several assembly cofactors , including Era, RbfA, RimJ, RimM, RimP, and RsgA, which associate with the 30S subunit, and CsdA, DbpA, Der, and SrmB, which associate with the 50S subunit. These subunits would have no function of their own, why then would random processes produce them without a final goal and no forsight of function ?

Five following conditions would all have to be met:
Kairosfocus
C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination.
Besides the implications for biomedical research, another consequence of the ribosome work was to resolve an old “classic chicken and egg problem” about evolution,
J.Sarfati :
the DNA information requires a complex decoding machine, the ribosome, but the instructions to build ribosomes are on the DNA. And decoding requires energy from ATP, built by ATP-synthase motors, built from instructions in the DNA decoded by ribosomes … “vicious circles” for any materialistic origin theory, as leading philosopher of science Karl Popper put it .

http://newswire.rockefeller.edu/2013/08/14/structural-biologist-interested-in-ribosome-assembly-to-join-rockefeller-faculty/
What’s more, it’s something of a chicken-and-egg problem. “You need the machinery to be in place in order to manufacture proteins, but the machinery itself is made of proteins that must be manufactured,” Klinge says.

Shajani Z : :A ribosome consists of 50–70 different components and is, therefore, one of the most complicated structures known in biology. The large number of components requires a highly coordinated synthesis and assembly.

The parts must be coordinated in just the right way: even if all of the parts of a ribosome are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits  are put together in the right order, they also need to interface correctly.

Resumed : For the assembly of a Ribosome, following steps must be explained : the origin of the genome information to produce all Ribosome subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or /  and evolution,  since we observe all the time minds capabilities producing ribosome-like machines and factories, producing machines and end products.


http://www.ncbi.nlm.nih.gov/pubmed/21529161
Shajani Z :
A ribosome consists of 50–70 different components and is, therefore, one of the most complicated structures known in biology. The large number of components requires a highly coordinated synthesis and assembly.


http://www.nobelprize.org/educational/medicine/dna/a/translation/ribosome_ass.html

This example of the Rate of Ribosome Synthesis is quite startling:

*HeLa cells (a type of human tumour cells) divide each 24 hours.
* Each cell contains around 10 million ribosomes, i.e. 7000 ribosomes are produced in the nucleolus each minute.
*Each ribosome contains around 80 proteins, i.e. more than 0.5 million ribosomal proteins are synthesised in the cytoplasm per minute.
*The nuclear membrane contains approximately 5000 pores. Thus, more than 100 ribosomal proteins are imported from the cytoplasm to the nucleus per pore and minute. At the same time 3 ribosomal subunits are exported from the nucleus to the cytoplasm per pore and minute.




http://sws1.bu.edu/mfk/ribosome.pdf




Althougheven this basic pathway is very complicated, translation involves many other features that have also been the subject of structural and functional studies in recent years. These include the rescue of stalled ribosomes, programmed frameshifting, the interaction of the nascent peptide with the exit tunnel, the modification of the peptide as it emerges from the ribosome, its folding and its transport across or insertion into membranes, and the regulation of translation. the extremely complicated field of eukaryotic translation, especially initiation, is sure to be increasingly targeted by biophysical and biochemical techniques.

Overview of bacterial translation. For simplicity, not all intermediate steps are shown. The colour scheme shown here is used consistently throughout this review. aa-tRNA, aminoacyl-tRNA; EF elongation factor; IF, initiation factor; RF, release factor.


Ribosomes composed of two subunits

3d:
http://www.rcsb.org/pdb/explore/jmol.do?structureId=2WDK&split=yes&asymIds=2WDK%2C2WDL%2C2WDM%2C2WDN&bionumber=1



A Ribosome is composed of two subunits, made of RNA chains with proteins bound on the outside.  The molecular movements of this complex provides a specific catalyst for the creation of amino-acid polymers.   These biological nanomachines are the 3D printers of the cell, producing thousands of different proteins.

http://cellmorphs.tumblr.com/


A Ribosome is composed of two subunits, made RNA chains and proteins bound on its outside.  The molecular movements of this complex provide a very specific catalyst for the creation of amino-acid polymers.   These biological nanomachines are the 3D printers of the cell, producing thousands of different proteins.

Ahh, the mighty ribosome. A biological machine comprised of an elaborate conglomeration of intricately-folded proteins and RNAs, none capable of building anything on its own, but together creating nature’s most advanced piece of chemical machinery.

It’s a fascinating chicken-and-egg problem written in nucleic and amino acids, a thing that has to exist in order to make itself


It’s also a thing that has to exist to make any of us, the translator of the genetic code, taking the instructions for life and assembling the things that do stuff inside of all of life.

When I look at this, I see the incredible beauty of evolution Gods creation  written in chemistry.

http://cshperspectives.cshlp.org/content/4/4/a003681.full
The molecular evolution of translation poses at least three difficult questions: (1) The chicken-or-the-egg problem: if the ribosome requires proteins to function, where did the proteins come from to make the first ribosome? (2) What was the driving force for evolution of the ribosome? and (3) How did coding arise? Thanks to numerous advances in this field, we now have a likely answer to the first question and a plausible basis for answering the second. Despite many decades of thinking about the third question, the origins of coding remain a puzzle. Another question, implicit in the RNA World hypothesis, is (4) Can we account for...

Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome, but Prefer Evolution-of-the-Gaps

Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics, similarly marveled at the complexity of the ribosome:

The ribosome, both looking at the past and at the future, is a very significant structure,  it's the most complicated thing that is present in all organisms.It can change from DNA three nucleotides into one amino acid. That's really marvelous. We need to understand that better.

Craig Venter suggested that by sequencing the genomes of more organisms perhaps we could reconstruct a primitive precursor ribosome. But Church is skeptical that this is unlikely to help because current biology reveals that a minimum number of genes are required for a functional ribosome--and that minimum number is still quite large:

But isn't it the case that, if we take all the life forms we have so far, isn't the minimum for the ribosome about 53 proteins and 3 polynucleotides? And hasn't that kind of already reached a plateau where adding more genomes doesn't reduce that number of proteins?

The conversation that follows is striking, showing that as far as we know, the ribosome has "irreducibly complexity":


   VENTER: Below ribosomes, yes: you certainly can't get below that. But you have to have self-replication.

   CHURCH: But that's what we need to do -- otherwise they'll call it irreducible complexity. If you say you can't get below a ribosome, we're in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins.

   VENTER: In the RNA world, you didn't need ribosomes.

   CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins.

   VENTER: Yes.

   SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously.

   CHURCH: It won't form spontaneously; we'll do it bit by bit.

   SHAPIRO: Both are obviously products of long evolution of preexisting life through the process of trial and error.

   CHURCH: But none of us has recreated that any.

   SHAPIRO: There must have been much more primitive ways of putting together

   CHURCH: But prove it.

We don't know how the ribosome and its required proteins evolved, but we know that "Both are obviously products of long evolution of preexisting life through the process of trial and error." This is a prime example of "evolution-of-the-gaps,"



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Nobel Prize Winner Cites the "Ingeniously Designed" Architecture of the Ribosome

In 2009, Israeli structural biologist Ada Yonath shared the Nobel Prize in Chemistry for her work on the structure and function of the ribosome. More recently, she had this to say about the "ingeniously designed" architecture of the ribosome:

Ribosomes, the key players in the translation process, are universal ribozymes performing two main tasks: decoding genetic information and polymerizing amino acids. Hundreds of thousands of ribosomes operate in each living cell due to the constant degradation of proteins through programmed cell death, which is matched by simultaneous production of proteins. For example, quickly replicating cells, e.g. liver cells, may contain a few million ribosomes. Even bacterial cells may contain [up] to 100,000 ribosomes during their log period. Other constituents are the mRNA chains, produced by the transcription of the segments of the DNA that should be translated, which carry the genetic information to the ribosomes, and tRNA molecules bring the cognate amino acids to the ribosome. To increase efficiency, a large number of ribosomes act simultaneously as polymerases, synthesizing proteins by one-at-a-time addition of amino acids to a growing peptide chain, while translocating along the mRNA template, and producing proteins on a continuous basis at an incredible speed, namely up to 20 peptide bonds per second.

Ribosomes are giant assemblies composed of many different proteins
(r-proteins) and long ribosomal RNA (rRNA) chains. Among these, the RNA moieties perform the two ribosomal main functions. The ratio of rRNA to r-proteins (~2:1) is maintained throughout evolution, except in mitochondrial ribosome (mitoribosome) in which ~half of the bacterial rRNA is replaced by r-proteins. Nevertheless, the active regions are almost fully conserved in all species. In all organisms ribosomes are built of two subunits, which associate to form the functionally active ribosomes. In prokaryotes, the small subunit, denoted as 30S, contains an RNA chain (16S) of ~1500 nucleotides and ~20 different proteins. The large subunit (50S in prokaryotes) has two RNA chains (23S and 5S RNA) of about 3000 nucleotides in total, and different >31 proteins. The available three dimensional structures of the bacterial ribosome and their subunits show that in each of the two subunits the ribosomal proteins are entangled within the complex rRNA conformation, thus maintaining a striking dynamic architecture that is ingeniously designed for their functions: precise decoding; substrate mediated peptide-bond formation and efficient polymerase activity.



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http://cshperspectives.net/content/2/9/a003483.full

By the time of LUCA, the ribosome clearly exists in essentially its modern form.Thus, laboratory reconstructions will be needed. However, there would be limited value in resurrecting the complete ribosome of LUCA, because it was in effect a modern ribosome itself.

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5 Origin and Evolution of the Ribosome on Wed Apr 09, 2014 4:53 pm

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When opponents of special creation asked about how x arised, they often make a quick web search, come up with the first search result which looks like a " serious " scientific paper, which explains how x evolved, and post it as a answer. When asked to quote the relevant part of the paper, which convinced them evolution were the best answer, commonly they don't answer, because they did not make the effort to analise carefully the proposed evidence. That shows nicely their confirmation bias. They determined already evolution must be true, since it fits their preconceived and wished world view, so all they do, is to try to fit everything they find into their naturalistic world view, without carefully looking if the evidence is compelling. Most scientific papers on evolution are perfect examples of how methodological naturalism works, and obliges specially historical sciences to wear blinkers. Since evolution is the only naturalistic possible explanation for the biodiversity on earth, evolution is supposed to be the answer right from the beginning, rather to start with a agnostic standpoint , and after careful examination, permitting the evidence to lead wherever it is, and propose evolution as the best explanation if that is the outcome that fits best. These pappers start with evolution, end with evolution, and in the middle is a not rarely high concentration of guess work, ad hoc explanations , and fairy tale stories.

Origin and Evolution of the Ribosome

http://cshperspectives.net/content/2/9/a003483.full

Abstract :   likely, it is argued, were likely, likely order, may have, Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed

The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely the guesswork begins    Very Happy  lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

and as final not of the paper :
In the end, no matter how complete a picture is developed of ribosomal development over time it will be hypothetical. The ultimate issue will be to prove at least the major parts of it. Thus, laboratory reconstructions will be needed. However, there would be limited value in resurrecting the complete ribosome of LUCA, because it was in effect a modern ribosome itself.



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6 The Miracle of Ribosome Assembly Evolution on Sat Apr 12, 2014 7:06 pm

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http://darwins-god.blogspot.com.br/2010/12/miracle-of-ribosome-assembly-evolution.html

New research is uncovering the details of how the cell’s protein factory—the ribosome—is constructed. The ribosome translates messenger RNA molecules—edited copies of DNA protein-coding genes—into a string of amino acids, according to the genetic code. The ribosome has two major components (one smaller and one larger), each made up of both RNA and protein molecules, and is constructed via a complex sequence of events.

The RNA components of the ribosome are copies of DNA genes. These ribosomal RNA molecules—known as rRNAs—are initially in a raw copy of DNA which eventually is edited. For instance, one of these copies of DNA may contain many rRNAs, separated by spacer segments. The spacer segments need to be removed, leaving the individual rRNAs ready for assembly.

One of the findings of the new research is that in the early stages of assembly, one of the DNA copies folds up such that a spacer segment binds to one of the rRNAs. In particular, the spacer binds to the special segment of the rRNA that reads the messenger RNA molecules, in the final, assembled ribosome. When the spacer is removed, the rRNA switches to its correct shape, for function in the ribosome. One implication of this finding is that ribosome construction can be regulated by this switch. Remove the spacer and ribosome construction proceeds. Leave the spacer, and ribosome construction halts. As the researchers concluded:

our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.


RNA tends to fold up into a variety of shapes. In this case, as lead researcher Katrin Karbstein suggests, RNA folding properties are part of the design:

Perhaps, nature has found a way to exploit RNA’s Achilles’ heel—its propensity to form alternative structures … Nature might be using this to stall important biological processes and allow for quality control and regulation.

But of course this mechanism brings yet more complexity:

What is interesting is that as the organism becomes more complex, the number of cleavages needed increases. This may make the process more accurate and that may be an evolutionary advantage, but even in bacteria this cutting is not done in a simple way. We still don’t know exactly why that is.


Karbstein suggests that the strictly ordered cutting and pasting steps in ribosome assembly are introduced to produce singularly perfect intermediates. As she explains:

Ribosomes make mistakes rarely, on the order of one in 10,000 amino acid changes. A lot of this accuracy depends on conversations between different parts of the ribosomes, so if the structure of the RNA isn’t correct, these conversations can’t happen. And that means more mistakes, and that’s not good because it can lead to any number of disease states.


Ribosomes don’t just happen. They are not easily assembled and the evolution of this choreography calls for several just-so heroics. Yes, this fine-tuned set of mechanisms makes for fantastic regulation of the cellular protein making factory, but it means that evolution must have gone through a stage where life didn’t work. For the spacer segment that binds to the rRNA is a show-stopper. It would be selected against instantly.

The only way to resolve this problem is to have the spacer removal mechanism already in place, before the spacer sequence itself evolved. As usual, evolutionists would need to rely on the needed mechanism just happening to serve some other useful purpose, and when the spacer sequence happened to arise for no reason, the removal mechanism found new work for itself. In other words, mutations arose that caused the DNA copy to fold, rendering ribosome synthesis—and life itself—impossible. But as luck would have it, there just happened to be the right molecular machine lying around that removed the problematic segment at just the right time and place. Not only was the fatal flaw obviated, but a brilliant new means of regulation invented. Amazing. Over time, further mutations happened to refine its actions and today we have the fine-tuned ribosome assembly process.

There you have it—evolution’s just-add-water version of science. For the umpteenth time evolution becomes a charade. Behind the scenes, in deep-time where no one can see it working, evolution once again performs miracle after miracle.


An RNA conformational switch regulates pre-18S rRNA cleavage.


Abstract


To produce mature ribosomal RNAs (rRNAs), polycistronic rRNA transcripts are cleaved in an ordered series of events. We have uncovered the molecular basis for the ordering of two essential cleavage steps at the 3'-end of 18S rRNA. Using in vitro and in vivo structure probing, RNA binding and cleavage experiments, and yeast genetics, we demonstrate that a conserved RNA sequence in the spacer region between the 18S and 5.8S rRNAs base-pairs with the decoding site of 18S rRNA in early assembly intermediates. Nucleolar cleavage at site A(2) excises this sequence element, leading to a conformational switch in pre-18S rRNA, by which the ribosomal decoding site is formed. This conformational switch positions the nuclease Nob1 for cytoplasmic cleavage at the 3'-end of 18S rRNA and is required for the final maturation step of 18S rRNA in vivo and in vitro. More generally, our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.

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7 Perfectionist protein-maker trashes errors on Sat Apr 12, 2014 10:11 pm

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But the Ribosome is fascinating, and worth a closer look about its amazing properites and functions :

http://www.hopkinsmedicine.org/news/media/releases/Lost_In_Translation

The Ribosome: Perfectionist Protein-Maker Trashes Error

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist

Johns Hopkins researchers, reporting in the journal Nature January 7, have discovered a new "proofreading step" during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a "delete" button.

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.

To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. "The cell is a wasteful system in that it makes something and then says, forget it, throw it out,"

That looks all ingeniously designed....... :smile: :smile: :thumbup:

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http://www.evolutionnews.org/2012/03/study_questions057501.html

The Ribosome
The ribosome is an intricate, complex protein and RNA structure containing two subunits that fit together like two hands in a cupped clap. The "cup" that the hands make is an empty space through which messenger RNA (mRNA) passes, is read, and translated into an amino acid connected to transfer RNA (tRNA).

The authors of the study propose that the individual sub units of the ribosome evolved separately but each subunit co-evolved with ribosomal RNA (rRNA) and then with the portion of the tRNA molecule that the modern-day subunit interacts with (the particular binding sites). The authors propose that these separate and simpler systems were co-opted very early in primordial history to form the machinery that we see today.

Co-Evolution of Ribosomal Proteins and RNA
The authors provide the following lines of evidence for the co-evolution of ribosomal proteins and RNA:

(1) Traditionally, the PTC active site has been considered the oldest part of the ribosomal protein. The idea behind stems from function, as well as an assumption that the proteins were built up in a step-by-step fashion. If this was the case, the outer components are likely "newer." The authors instead looked at the tertiary structure and employed studies using structural similarities to determine evolutionary age:

   In contrast, here we infer the history of the complete RNP ensemble using phylogenetic methods that employ standard cladistics principles widely used for example in the analysis of morphological characteristics of organisms. Shared-derived features of structure defined by crystallography and comparative sequence analysis are treated as phylogenetic characters and used to build structural phylogenies.

The authors found that due to the age difference in portions of the ribosome, there was likely a functional core that pre-dates the PTC active site. This particular study raises some red flags, however, because homology (structural or genetic similarities) is a tricky thing. Usually evolutionary biologists apply homology to organisms.

(2) The authors' studies indicate that the ribosome subunits may have originally interacted separately until a "major transition" occurred that brought the subunits together. This "major transition" coincided with the evolution of tRNA. These studies dealt with the supposed evolution of the inter-subunit bridge through which the two subunits interact. The authors note that any mutations to this bridge leads to non-functionality.

(3) Tertiary interactions between RNA-RNA and RNA-protein occurred after the first major transition.

   We propose that A-minor and other tertiary interactions evolved to stabilize and maintain the ribosome structure during elongation, leading to increased ribosomal processivity. Scarcity of A-minor interactions before the major transition implies that the early proto-ribosome structure was mostly stabilized by r-proteins or their precursors.

(4) According to authors' studies, tRNA is at the center of ribosomal evolution. There are two major sections of tRNA and each one interacts almost exclusively with a particular subunit of the ribosome. These RNA/subunit partners evolved individually, then came together to form the modern-day complex sometime after the first major transition. The modern-day complex was built around tRNA:

   These remarkable patterns suggest that subunit interactions with a full modern cloverleaf tRNA structure were recruited for translation after the major transition and that the ribosome was built around tRNA or tRNA-like structures...

(5) Phylogenetic studies show that the oldest parts of the ribosome interact with the oldest parts of the ribosomal RNA (rRNA), and the evolution of these two are "linked" in such a way that as one evolves so does the other. The authors state that this is evidence for their co-evolution and believe that this intimate interaction is the reason why ribozyme studies have not progressed:

   We propose complex ribosomal functionality emerged from the cooperative interaction of rRNA and r-proteins (or their precursors), which existed from the earliest stages of ribosome evolution. Thus far, in vitro peptidyl transferase activity catalyzed by protein-free rRNA derived from extant rRNA or ribozymes is not demonstrated. Perhaps, the primordial cooperative property of the RNP complex explains why such attempts have failed.

The same evidence, however, could also show that these structures are irreducibly complex, rather than that they co-evolved.

(6) A second major transition occurred in which ribosome evolution coincides with the emergence of a particular protein complex that "stimulates the GTPase activity of EF-G, a ribosomal factor that catalyzes elongation and is responsible for marked increases in the processivity of the ribosome." In other words, this transition has to do with important specific activities involved in building proteins.

(7) The ribosomal core has components that are similar to ribozyme-like activity and therefore provide evidence for recruiting various parts to form the translation system, or co-option:

   Thus, it is likely that the ribosomal catalytic core had origins in processive substructures common to replication and translation and is a descendant of a primitive templating complex...Since structural components of a proto-ribosome involved in tRNA, mRNA and intersubunit interactions are older than others, these results also support the replicative origin of tRNA.

( 8 ) Certain components, such as translation initiation factors, tRNA binding proteins, DNA binding proteins, and telomere binding proteins have a similar folding arrangement, and therefore likely have a common origin:

   RNA binding and DNA binding proteins therefore have a common evolutionary origin, suggesting ancient r-proteins and homologs were originally part of primitive replication machinery, which diversified and was co-opted for modern translation. This ancient replicative function most likely involved processivity and biosynthetic activities that we believe remain hidden today in ribosome function." (emphasis added)

Unfortunately, while the authors suggest co-option, they do not have a model system on which to base the prior function of these mechanical parts, which makes this highly speculative.

Assessment
Overall, the authors appeal to co-option and co-evolution and justify this using phylogenetic homology studies. They contend as many in the ID camp do that "the de novo appearance of complex functions is highly unlikely. Similarly, it is highly unlikely that a multi-component molecular complex harboring several functional processes needed for modern translation could emerge in a single or only a few events of evolutionary novelty." Their explanation, however, is that a simpler system was performing a different function, and then was recruited into the complex protein translation machine.

The question that follows is what exactly did the recruiting? What provokes recruitment to another system? The authors labeled this time of recruitment the "first major transition" but their explanation of the transition is a little cloudy.

They seem to answer the question of "motivation to recruitment" by appealing to co-evolution. The RNA and ribosome proteins are co-dependent such that as one evolves, the other does too and somehow it reached a point where a "major transition" occurs.

There are many striking features of this study, such as the authors' acknowledgement of the deficiency of ribozymes to account for the "chicken-and-egg" problem with protein synthesis, and their recognition of the improbable evolution of RNA apart from the ribosomal protein in view of the fact that the relevant functions are so intimately intertwined.

While these results show a relationship and even a correlation between tRNA and the ribosome, it is still unclear what exactly promoted recruitment, what attracted the tRNA to the proto-ribosome, or why co-option must be the conclusion. Could this not also be a case of an irreducibly complex machine?

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Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis

Ribosome synthesis in eukaryotes requires a multitude of trans-acting factors. These factors act at many steps as the pre-ribosomal particles travel from the nucleolus to the cytoplasm.

Ribosome biogenesis is a fundamental multistep process that, in eukaryotes, takes place largely within the nucleolus.Late steps in both 40S and 60S ribosomal subunit (r-subunit) synthesis occur in the nucleoplasm and after nuclear export of precursor particles in the cytoplasm . Ribosome synthesis is evolutionarily conserved throughout eukaryotes , and so far most of our understanding of this process has been obtained from studies with Saccharomyces cerevisiae . In the yeast nucleolus, three of the four rRNA(18S, 5.8S and 25S) are transcribed as a single large primary transcript by RNA polymerase I and processed to the first detectable rRNA precursor (pre-rRNA), the so-called 35S pre-rRNA. The fourth rRNA (5S) is independently transcribed as a pre-rRNA (pre-5S) by RNA polymerase III. In the 35S pre-rRNA, the mature rRNA sequences are separated by two internal transcribed spacers (ITS1 and ITS2) and flanked by two external transcribed spacers (5′ ETS and 3′ ETS), which must be precisely and efficiently processed to ensure correct formation of mature rRNAs . Maturation of rRNAs is a well-defined pathway  and involves numerous trans-acting factors that are required for the processing and covalent rRNA modification reactions, such as small nucleolar RNA–protein (snoRNP) complexes, endonucleases and exonucleases, and different base methylases . Concomitantly to rRNA maturation, the pre-rRNAs assemble in an ordered manner with the 79 ribosomal proteins (r-proteins) and a large number of trans-acting factors that are generally referred to as r-subunit assembly factors  (for examples of trans-acting factors see http://www.medecine.unige.ch/~linder/proteins.html). The process of r-subunit assembly is still poorly understood. An outline of this process was provided by sucrose density gradient analyses in the 1970s, which identified 90S, 66S and 43S pre-ribosomal particles . Recent advances employing proteomic approaches have revealed several distinct, successive pre-ribosomal particles and refined the model for the maturation of both 40S and 60S r-subunits [for a review . These proteomic approaches have also led to the identification of novel non-ribosomal proteins, increasing the number of trans-acting factors involved in ribosome biogenesis to over 180. Evidence towards an understanding of the function of many of these trans-acting factors has been obtained by using a complete repertoire of techniques, thus, addressing their temporal association with pre-ribosomal particles and revealing the pre-rRNA processing and nucleocytoplasmic export defects caused by their mutational inactivation or depletion .

http://www.ncbi.nlm.nih.gov/pubmed/21529161
Ribosome assembly needs  the contributions of several  assembly cofactors , including Era, RbfA, RimJ, RimM, RimP, and RsgA, which associate with the 30S subunit, and CsdA, DbpA, Der, and SrmB, which associate with the 50S subunit.



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http://www.reasons.org/articles/proteins-made-by-design-part-1-of-3

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http://rnajournal.cshlp.org/content/10/12/1833.full

recent crystallographic studies have revealed the ribosome to be a structure of unprecedented complexity

Most importantly, they cannot have evolved initially to make functional proteins, in the modern sense, because of the vanishingly small probability that the first attempts at polypeptide synthesis by a primitive translational apparatus could yield a protein with any useful enzymatic activity (Woese 1967).

That is to say, the RNA world could not have anticipated that the evolution of a macromolecular machine with the complexity of the ribosome would in turn eventually lead to the evolution of long polypeptide chains of specific sequence that fold into stable, three-dimensional structures with desirable biological functions. Clearly, until the first active proteins emerged, no selective advantage would exist for evolution of a translational machinery, if its only purpose was to synthesize functional proteins.

Yet, we know it evolved, because here it is ( funny, as if there were no other options, like special creation...... )

More likely, protein synthesis initially arose not to create fully functional enzyme-like proteins, but for some other purpose. ( how do they know ? )

Specification of amino acids by RNA sequences most likely emerged later, requiring coevolution of the ribosome and its tRNAs (Noller 1993; ( further guesswork... nice ! )

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Ribosome Checks for Translation Errors (and a bunch of other stuff)

1

There is a vast network of information flow in a typical cell, and along with that flow there is a vast network of error checking. Damage to DNA sequences is remedied, the transcribing of DNA is checked and corrected, and at the ribosome the translation process is checked and controlled. In fact, recent research has found that the ribosome not only carefully sets up the codon-to-amino-acid translation process for success, but if an error is made the ribosome detects it and takes action after the translation process.

When the ribosome detects a translation error it takes action 10,000 times faster than it normally does. "These are not subtle numbers," explained the lead researcher. As one report explains, "the ribosome exerts far tighter quality control than anyone ever suspected."

How does the ribosome do it? The ribosome--which creates proteins--consists of RNA and protein molecules. If the ribosome is the machine that builds proteins, then from where did the ribosome's proteins come in the first place? Evolutionists believe that initial versions of the ribosome--the proto-ribosome--had only the RNA molecules and the proteins came later.

Perhaps so, but the translation task is not simple, and the ribosome's proteins do not appear simply to be innocent bystanders that evolution, for no particular reason, kludged onto the ribosome. Rather, the proteins are deeply embedded in the ribosome, and appear to be important for both the ribosome's structure construction and conformation. This is probably why RNA-only proto-ribosomes don't seem to work.

But this is not all. Even ignoring the problem of obtaining an RNA-only translation machine, the evolutionary hypothesis raises the question: From where did the protein-coding sequences come which it would translate? In other words, even if a long sequence of RNA residues just happened to assemble and fold and function as a proto-ribosome, why would it be selected for if there were no protein-coding sequences lying around? One could add to this a long list of other requirements, such as a ready made pool of amino acids, and of course something for the newly minted protein to do.

Of course evolutionists can always speculate. For instance, perhaps a functional RNA molecule just happened to also code for a useful protein. How convenient.

Fortunately, in a world where confessions of evolution's heroics are rare, one nobel laureate scientist gave this judicious observation: "How evolution managed to progress from making a random peptide to messenger-directed synthesis, we haven't a clue." And yet evolution is a fact? I think I want my money back.

1) http://darwins-god.blogspot.com.br/2010/01/ribosome-checks-for-translation-errors.html

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A . Earliest Beginnings: RNA World

1. Initial Formation of Peptidyl Transferase Center in RNA World
A. Emergence of RNAs that can aminoacylate RNAs -leads to small charged
RNAs (minihelices)
B. Emergence of RNAs that can catalyze peptide bond formation between minihelices.
2. Beginnings of coherent SOS subunit
Portions of Domain V of 23S rRNA likely present. Addition of more RNA or
essentially random peptides might have decreased hydrolysis reaction and increase
activity by protecting the core reaction.
3. Extension of tRNA to two domains;
Second tRNA domain allows templating, which significantly increases reaction rate.
Characteristic conformational changes associated with translocation are present.
4. Beginnings of coding
It is now possible to store information. This makes it useful to have a genome (RNA)
and hence primitive polymerases might offer a significant selective advantage to
progenotes that have them.
B. Beginnings of Transition to Protein World: Late RNA World
5. Ancestors of core proteins such as L3 and L4 are present.
Emergence of defined sequence peptides means RNA World will soon end.
6. Initial creation of 30S particle
Further protection of the reaction machinery is possible by stabilizing template.
Bridges between subunits were probably initially only RNA. Portions of Domain IV
of 23S rRNA that interact with 30S subunit are likely to be present.
C. Early Protein World: Major Refinements Increase Speed and Accuracy
7. EF-Tu ancestor
Improved control of tRNA access to machinery
8. Addition of 5S rRNA complex
Further development of SOS subunit underway. Many new proteins present such as LS
and LI 8 that are associated with SS rRNA incorporation
9. GTPase Reaction Center Formed
The emerging protein world allows the development of the translocation machinery.
LI 0 now present. At least portions of 23S rRNA Domain II are present.

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Molecular basis for protection of ribosomal protein L4 from cellular degradation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5296656/


Eukaryotic ribosome biogenesis requires the nuclear import of ∼80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone–substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function tofacilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery.

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Two proofreading steps amplify the accuracy of genetic code translation

http://www.pnas.org/content/113/48/13744.abstract

We have discovered that two proofreading steps amplify the accuracy of genetic code reading, not one step, as hitherto believed. We have characterized the molecular basis of each one of these steps, paving the way for structural analysis in conjunction with structure-based standard free energy computations. Our work highlights the essential role of elongation factor Tu for accurate genetic code translation in both initial codon selection and proofreading. Our results have implications for the evolution of efficient and accurate genetic code reading through multistep proofreading, which attenuates the otherwise harmful effects of the obligatory tradeoff between efficiency and accuracy in substrate selection by enzymes.

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