June 25, 2020 | Jerry Bergman

Origin of the Ribosome Baffles Evolutionists

 

 

The Ribosome. Life Cannot Live Without it. How Did it Evolve?

by Jerry Bergman, PhD

Figure 1. A diagram of a ribosome showing its enormously complex structure. From Fvoigtsh via WikiCommons.

 

Introduction

The ribosome is a macromolecular machine used by all living cells, both prokaryotes like bacteria and eukaryotes, including all vertebrates from fish to humans. The cell requires ribosomes to convert the DNA instructions into the functional proteins that make up all life. A cell cannot survive without ribosomes, each of which contains thousands of parts, all of which must be manufactured and assembled to exacting specifications. Every second of every day, all life’s [or living] cells are making proteins based on the information stored in its DNA. It is for this reason an animal cannot live until all of its billions of parts, including the ribosome, are manufactured and properly assembled.  Even though DNA is described as having “massive intelligence . . . by itself [it has] neither a future nor a present. DNA without a cell to sustain and express it has no physiologic meaning.”[1] The structure of the ribosome, which was solved only in the year 2000

revealed that it is still at heart a ribozyme [an RNA molecule capable of acting as an enzyme], with RNA elements still carrying out its essential function, establishing a peptide bond. Why, then, did it grow to such an unwieldy size and incorporate so many proteins into its structure? Real-time observation of its assembly under physiological conditions has some surprising answers.[2]

This feat revealed that the “ribosome is the most complex molecular machine shared by all cellular life forms.… researchers can now study the assembly of the [ribosome] structure in real time, yielding further insights into the origins of complexity” of this machine.[3] And what they are learning has given evolutionists a big headache. As you read this brief description of how the ribosome system produces protein according to the code contained in DNA, it is clear that, first, the system will not function as a ribosome until all of its millions of parts exist and are properly assembled. Then I will explain the failed attempts to explain the evolution of this system that must exist in all living cells.

Human genes are estimated to be, on the average, 40,000 base pairs (bp) long including control sequences and introns. Gene lengths range from 1,480 bp for the somatostatin gene to over 2,000,000 bp for the dystrophin gene. Most genes range from 300 to 3,000 bp.[4] To produce a functional protein, the 20 necessary amino acids must be assembled into the order required to produce polypeptide chains that fold according to the specific amino acid positions on the amino acid chains.[5] The animal body is made up primarily of proteins.

Ribosomal RNA and Ribosomes

Ribosomes are “extremely complex” protein synthesis machines that serve as peptide chain assembly jigs to ensure the proper attachment, alignment, and securement of the amino acid building blocks.[6] The ribosome consists of about 50 proteins and special RNA called ribosomal RNA (rRNA). Ribosomes are differentiated by size; their subunit parts designated in terms of solid sedimentation rates. The time it takes for a particle to settle out of solution is measured as a sedimentation coefficient in Svedberg (S) units, where 1S = 10-13 seconds. Since Svedberg units represent settling rates, and not particle weights, they are not additive. For example, prokaryotic ribosomes use a 70S ribosome made from two parts, a large 50S subunit and a small 30S subunit, whereas eukaryotic ribosomes use the slightly larger 80S type composed of a large 60S and a small 40S subunit. Ribosomes are all metalloenzyme dependent, principally on divalent magnesium (Mg2+ ion ). The ribosome contains enzymatic proteins and three different sections of RNA that are exactly 120, 1,542 and 2,904 nucleotides long.[7] The structure functions as a frame to control the conversion of the DNA base code into a set of amino acid chains, a process called translation.

The RNA molecule is very similar to the DNA molecule, but has a ribose sugar backbone and uses the uracil base instead of thymine. One type of RNA called messenger RNA (mRNA) carries the code stored on a DNA molecule to the protein manufacturing sites on the ribosomes.  The mRNA is usually from about 70 to several thousand nucleotides in length. The half-life of mRNA is only about 1 to 5 minutes, a fact helping to control protein production.[8]  Because of this short half-life, about half of all RNA synthesized is mRNA yet it consists of only three percent of cellular RNA at any one time.

Figure 2. A cartoon diagram of the ribosome in action.

 

DNA length ranges from several thousand to about a billion nucleotides long, depending on the organism. In humans, the total nucleotide length is three billion bp. Bacteria contain several million DNA nucleotides, the simpler eukaryotes such as fungi contain a half billion, and some flowering plants contain several hundred billion.[9]

The ribosome also must find the proper section on mRNA to begin translation. In prokaryotes this site is marked by a set of bases called the Shine-Dalgarno Sequence which is located about ten bases upstream from the initiation site. The initiation site begins at the first subsequent AUG sequence made from the DNA bases Adenine, Uracil and Guanine. The AUG sequence is the start codon but also codes for the amino acid methionine. In eukaryotes, the initiation usually begins at the first AUG sequence on the mRNA, but is a simpler system than used in the prokaryotes; the opposite of what evolution predicts! The methionine that AUG codes for usually has to be removed from the polypeptide before the chain is completed.

In prokaryotes, for the ribosome to bind requires three initiation factors labeled IF-1, IF-2 and IF-3. The IF-1 and IF-2 binds to the 30S ribosomal subunit. Then the larger subunit joins and this complex then must bind to a tRNA (transfer RNA) carrying methionine, then bonds to an IF-2 molecule and to the mRNA molecule on the initiation site. The eukaryote system is more complex involving as many as ten or more initiation factors. Lastly, the 50S subunit bonds to the RNA, causing the IF-1, -2 and -3 to fall off.[10]

Figure 3. tRNA showing the yeast eukaryote amino-acid structure and the four arm design when viewed from the top.

 

The mRNA first attaches to the smaller ribosome subunit, then the first tRNA is matched with the code. Next, the larger ribosome subunit connects to the smaller, and the second tRNA bonds with its matching mRNA code. As the mRNA slides through the ribosome, the tRNA lines up amino acids according to the codon and anticodon match. The anticodon is complementary to one of the codons for the amino acid it carries. The next step requires a tRNA molecule associated with an elongation factor TU protein (EF-TU) to carry its proper amino acid to bind to the ribosome.

Transfer RNA (tRNA)

The tRNA is a single strand of RNA between 73 and 93 nucleotide sections which folds back on itself so that its bases can hydrogen-bond to form the shape required to carry out its role in the cell.[11] Like proteins, the tRNA folds to produce the required three-dimensional shape, and is therefore sometimes humorously said to be an RNA that wanted to be a protein.

The tRNA functions to transfer the amino acids floating nearby to the growing polypeptide chain. A typical eukaryotic cell contains up to 100 different tRNAs, accounting for up to 15 percent of the total cellular RNA by weight. At least twenty tRNAs exist, one for each amino acid. Thus tRNA ala carries only alanine, etc.

The tRNA’s clover leaf secondary structure has four arms plus an acceptor stem. The acceptor end always consists of the bases CCA (cytosine, cytosine, alanine). The anticodon loop always possesses seven nucleotide residues. Attaching amino acids to the tRNA requires energy via a reaction catalyzed by specific enzymes called aminoacyl-tRNA synthetases, often called amino acyl-tRNA ligases. The cleavage of ATP generates AMP plus PPi. To attach the amino acid to its tRNA also requires a specific aminoacyl-tRNA synthetase, and, consequently, all cells must contain at least one aminoacyl-tRNA synthetase for each of the 20 protein amino acids. It selectively recognizes both a specific amino acid and a specific tRNA to which that amino acid should be attached. Aminoacyl-tRNA synthetase molecules are also large, very complex structures as are most all of the components of the process described here. A tRNA molecule to which an amino acid is attached is charged (chemically bonded) or aminoacylated. When its amino acid is released, it is uncharged.

The aminoacyl-tRNA synthetases rarely make a mistake, but when one occurs the system often recognizes the mistake and catalyzes the hydraulic removal of the improperly placed amino acid, a process called proofreading.[12] Amino acids are initially attached to the tRNAs by an ester link to either the two- or three-prime position of the ribose residue within the three-prime terminal nucleotide residue.

Next, a peptide bond forms between the two amino acids held by the two tRNAs partly due to the reaction of the high-energy bond between the activated amino acid and the tRNA formed due to ATP. The larger ribosomal subunit also contains the enzymes required for the peptide bond formation. Each added amino acid is connected to the chain by dehydration synthesis. Then the bond between the first tRNA and its amino acid is cleaved, and the second tRNA then moves into the ribosome site previously occupied by the first tRNA. Next, the ribosome moves down exactly three nucleotides, a step requiring a protein called elongation factor-G (EF-G).

The tRNA structure also uses several slightly modified bases such as inosine. The bases are modified after the tRNA strand is produced by special enzymes, including methylases, deaminases, thiolases, pseudourydylating enzymes and transglycosylases.[13] The correct amino acid bonds to its mate tRNA with the aid of enzymes called tRNA synthetases using energy from ATP.

Each tRNA type requires a specific tRNA synthetase and at least twenty different enzyme tRNA synthetases to exist. They function by, first, an ATP docking in a slot on the enzyme, then an amino acid docks nearby and is “charged” by the ATP losing two of its phosphates. The energized amino acid can now bond to the correct tRNA so that the proper place at the 3’ end of tRNA can bind.[14]  At least one tRNA molecule exists for each of the 20 amino acids.

Concurrently, the bond between the tRNA and its amino acid is then broken by hydrolysis. Finally, the empty tRNA floats away to be recharged so it can carry yet another amino acid to be bonded to the growing peptide chain. The mRNA is usually read by more than one ribosome (called a polysome or polyribosome for free ribosomes) simultaneously for efficiency. This allows more proteins to be made from a single mRNA before it is degraded. Protein synthesis often progresses at a rate of about 15 amino acids per second.  This process occurs until one of the three stop codons (UAA, UAG, UGA) is reached, and the two parts of the ribosome then separate, dropping off the messenger rRNA. Translation stops when the stop codes are reached because no tRNA exists for these three codes to which an anticodon can bond. A protein called a releasing factor competes for a mRNA base pair but does not bind if a tRNA exists for a codon triplicate.

The releasing factor results in the hydrolysis of the ester bond between tRNA and the polypeptide chain, releasing the completed polypeptide.[15] It then often undergoes post-translational modification, such as the addition of sugars called glycosylation or hydroxylation, the adding of hydroxyl groups to form hydroxyproline and hydroxylysine, respectively. Lastly, the protein chains undergo folding as discussed above. The mRNA itself is eventually broken down by a ribonuclease and its parts, mostly nucleotides, are recycled into new RNA strands.  The cell uses this system as one way of achieving tight control of protein synthesis. Gross adds that

Many proteins rely on molecular chaperones to avoid misfolding and aggregation. As the process of RNA folding and ribosome assembly is even more complex and error-prone, it is reasonable to expect that it receives similar help in the [ribosome] in the cell.[16]

Thus new research Gross describes only makes the process described above even more complicated.

Evolutionists’ Pathetic Attempt to Explain the System Just Described

This is only a brief  review of some of the major steps required to produce protein from the DNA instructions. The system will not work, and life will not survive until all of the parts or their counterparts described above, plus many more, exist, and are constructed within very narrow tolerances. Evolutionists have no idea how this complex system could have evolved as a functional unit. One recent effort will now be reviewed.[17] The evolution story is:

One day, more than three billion years ago, an RNA catalyst arose that could link amino acids together to form a peptide bond. This catalytic spark set the stage for the division of labor between nucleic acids and proteins that defines life today. Over evolutionary timescales, it also led to the most complex molecular apparatus found in cells — the ribosome.[18]

The essential conclusion of the new research is, because ribosomes are manufactured in sections, the sections evolved independently first and serve an enzyme function and, only later, came together to form the modern ribosome. Thus the ribosome parts performed only catalytic functions until they came together to function as a ribosome. The problem is, until the ribosome sections are assembled, the cell could not live. The ribosomes would serve no function without all of the other necessary parts of the system, including DNA, RNA, tRNA, mRNA and the thousands of other parts required. Furthermore, this new discovery Gross describes creates more problems for evolution, namely each domain of the ribosome must fold and assemble

sequentially as the RNA is produced by the RNA polymerase. This gradual build-up of structure can help with the problems to an extent. However, some key interactions in the RNA folding are between nucleotides far away from each other in the sequence, so there still is a risk of some misfolding while a given nucleotide is waiting for its intended binding partner to show up.[19]

Consequently, until its binding partner shows up and binds with the existing part to form a functional ribosome, another system has to be added to the cell to ensure the required parts are concurrently manufactured, sent to the correct location for assembly, directed in proper alignment for assembly until the bonding occurs, requiring a new set of specific enzymes to create the bond. This problem is confusing to describe, but in real life could not occur. All of the parts must exist and function as a unit for life to exist, and the partial assembly that comes together to produce a functional ribosome idea fails.

Conclusions

New research in biochemistry and cell biology consistently creates new problems for evolution. In addition to the natural-selection hurdles noted above, research groups led by André Schneider at the University of Bern and Nenad Ban of the ETH Zurich

have studied the assembly of mitochondrial ribosomes in the parasite Trypanosoma brucei, which causes sleeping sickness in humans [Science (2019) 365:1144–1149]. Its ribosome is remarkably different from the bacterial version in that it contains many more proteins and a reduced length of RNA strands.[20]

Not to be outdone, chemistry researcher and science journalist Michael L. Gross noted this research has added insight to

the common root of conventional phylogenetic trees, the last universal cellular ancestor (LUCA). Phylogeny tells us that LUCA already possessed a complex translation apparatus similar to the one that is still around in bacteria. On the assumption that this ancestral set of molecules evolved from duplications of a smaller set, research into tRNA synthetases, for instance, has led to deeper roots beyond LUCA, with just two different synthetases presumed to be the ancestors of today’s diversity.

In other words, the LUCA looks very much like that existing in modern bacteria, causing problems to the common molecules-to-man theory. A major plank in the creation worldview firmly supported by science is life must have been created fully-functionally complete and living in all its required complexity, ex nihilo from nothing.


References

[1] Kornberg, Arthur. 1989. For the Love of Enzymes. Cambridge, MA: Harvard University Press, p. 316.

[2] Gross, Michael. 2020. “How to Build Complexity.” Current Biology 30(10):R454-456, May 18, p. R454.

[3] Gross, 2020, p. R454.

[4] Jorde, Lynn B.; John C. Carey, and Raymond L. White. 1997. Medical Genetics. St. Louis, MO: Mosby, p. 39.

[5] Levine, Joseph S. and David Suzuki. 1993. The Secret of Life: Redesigning the Living World. Boston, MA: Wgbh Publishing..

[6] Frank-Kamenetskii, Maxim D. 1993. Unraveling DNA. New York, NY: VCH (Verlag Chemie), p. 20.

[7] Behe, Michael J. 1996 Darwin’s Black Box: The Biochemical Challenge to Evolution. New York, NY: The Free Press, p. 273.

[8] Zubay, Geoffrey L.; William W. Parson, and Dennis E. Vance. 1995. Principles of Biochemistry.  Dubuque, IA.: Wm. C. Brown Publishers.

[9] Behe, 1996, pp. 266, 268.

[10] Zubay, Geoffrey L., et al.,1995

[11] Mader, Sylvia S. 1993. Biology. Dubuque, IA: Wm. C. Brown Publishers, p. 256.

[12] Bergman, Jerry. 2005. “The Mutational Repair System: A Major Problem for Macroevolution.” CRSQ  41(4):265-273, March.

[13] Zubay, Geoffrey L., et al.,1995.

[14] Hoagland, Mahlon B.; and Bert Dodson. 1995. The Way Life Works. New York, NY: Random House, pp. 114-115.

[15] Singleton, Paul and Diana Sainsbury. 1994. Dictionary of Microbiology and Molecular Biology, 2nd ed. New York, NY: John Wiley & Sons, p. 712.

[16] Gross, 2020, p. R454.

[17] Gross, 2020, p. R454.

[18] Gross, 2020, p. R454.

[19] Gross, 2020, p. R454.

[20] Gross, 2020, p. R455. Emphasis added.


Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

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