Chapter 9

The Remarkable Way Cells Translate DNA

. . . to duplicate that which only God could conceive. ¹

—Diane Rothstein

PERIODICALLY NEWSPAPERS REPORT in bold headlines and in a variety of wordings that scientists have succeeded in “synthesizing life” in laboratory experiments.  What has usually happened, however, is that living cells have been taken apart, and then some of their components have been reassembled or combined with other chemicals.  In all such experiments to date, a vital part of success has depended upon one or more complex parts that grew in actual living cells.  (Even if the production of life from nonliving chemicals could be accomplished in the laboratory, it would be a product of intelligence, not chance.)
    C. L. Strong has said (1970), “No one has created life in the laboratory.  The possibility is vanishingly small that a viable organism can be compounded.  Yet that slender chance continues to intrigue some experimenters....”²  It was of these experiments that Diane Rothstein wrote in the above quotation.
    To bring our knowledge of the DNA system to the maximum needed before applying probability theory, this chapter will outline the fascinating process by which DNA translates information into action.

DNA Directs the Cell’s Activities

John Kendrew uses this fitting comparison:

Any living thing can be likened to a giant factory, a factory

producing chemicals, producing energy and motion, indeed reproducing itself too (which most factories cannot do!) and if one thinks of the way in which assembly lines are organized in factories one realizes immediately that all this complex of operations could not be carried out unless they were in some way organized, separated into compartments, not higgledy-piggledy.  In other words, there must be some kind of organization in the structure of an animal to enable it to carry out these processes in an orderly way.³

Transcribing From DNA to RNA Working Copies

We will follow Kendrew’s analogy of an industrial plant.  The DNA master copy of the production blueprints must be kept protected.  What is required first of all is a way to make working copies of just the sections needed at the moment.  These temporary copies can then be taken out into the rough-and-tumble of the production area, leaving the DNA original safely in the office.  When no longer needed, the copies are destroyed.
    The temporary copies of parts of the DNA are called RNA, or, more properly, messenger-RNA, usually written mRNA.  RNA is quite similar to DNA.  In fact, it is identical in structure to one-half of the DNA double helix, except in two respects.
    The difference in name comes from a very slight difference in the sides of the chains.  RNA is the abbreviation for ribonucleic acid.  DNA is deoxyribonucleic acid.  The small sugar molecules used in RNA are ribose sugar.  Those in DNA are deoxyribose, with one less oxygen atom.  (This slight difference is very important to life.  It keeps the DNA from being dismantled by the enzyme “ribonuclease,” which takes apart mRNA chains when their temporary job is completed.)
    There is one other difference.  The four RNA bases are the same as those used in DNA, except that in place of thymine, RNA always has uracil, which is quite similar.  RNA’s four bases

are, therefore, adenine, cytosine, guanine, and uracil—A, C, G, and U.
    The translation of DNA into proteins is done indirectly, via RNA.  The reason, as we have indicated, is that DNA, the vital carrier of hereditary information from generation to generation, must be kept safe from damage at all times.  This master copy of the instructions is therefore retained in the cell nucleus or otherwise protected.  The wisdom of this is apparent.

The Transcription Process

When a section of DNA is to be transcribed into RNA, the DNA double helix divides at that location into two strands. Then, an RNA chain forms alongside one of those strands, in the same way that DNA replication takes place.
    In the cell fluid are large numbers of the individual parts which can be used to form RNA chains.  These are called ribonucleotides or RNA nucleotides.  Each individual nucleotide will match one specific type of base in the divided DNA.
    The same complementary base-pairing plan works here as when DNA duplicates itself, as described earlier.  It must be remembered, however, that RNA uses uracil instead of thymine.  When RNA is forming alongside the DNA strand, the DNA adenine will pair with the RNA nucleotide uracil.  Here are the pairing possibilities:

enzyme is found in virtually all cells,⁴ and is called RNA polymerase.  It is responsible in large measure for the precision and fidelity of the copying process.  There is evidence that this copying accuracy is so exact that it might correspond to a typist’s making only one error in from 7 to 700 pages.⁵  As to speed, as many as 30 or 40 nucleotides per second may be added to the forming RNA chain, in bacteria.
    As the RNA copy is formed along the DNA pattern strand or template, it immediately separates progressively from the DNA.  The two DNA strands then join up again, thus returning to their normal double helix condition.⁶
    Before proceeding to what happens next with the RNA copy, two questions arise.  When are copies made, and where do they begin on the DNA template?

Turned-Off Genes and Sophisticated Controls

Although much remains to be learned, it is now clear that an elaborate and precise control system governs the timing and location of RNA transcriptions.
    That portion of DNA which encodes the sequence of one particular protein chain is called a gene.  Genes must be switched off when not needed or there would be utter chaos from overproduction of items.  While research is continually adding information, it is now clear that many genes are kept in the switched-off position by repressor molecules which are in turn coded for by regulator genes.  The job of a repressor is to fasten to the DNA at an operator site, thereby preventing any copying

of that gene into the form of RNA.  This complex system involves two or more methods of operation.  One technique employs molecules known as inducers, of which there are many kinds.
    An inducer molecule will combine by weak bonds with a specific repressor, and this keeps the repressor from fastening to the gene.  As a result, the repressor cannot turn off the gene, and so RNA polymerase begins transcribing that gene, by starting at a place on the DNA called the promoter.  Here is one example.  Suppose lactose sugar starts arriving outside of the cell of an Escherichia coli bacterium.  An inducer will then fasten to the repressor that controls the genes which produce enzymes for processing lactose.  As a result, the genes are transcribed into RNA, and proteins are formed for bringing lactose into the cell and processing it as food for the cell.  It is much more complicated than this, but in this intricate way, the transcription begins at the proper place at the start of a gene and continues for the length of one or more genes.⁷
    An alternative system works in this way: When there is on hand enough of a specific type of molecule used by the cell, one of those molecules will combine with a repressor, thereby causing it to fasten to the DNA at the operator site and keep the gene turned off because its product is not needed due to the supply already on hand.  In this case, the molecule which fastened to the repressor is a sample of the type that is in plentiful supply or a related metabolite, and this molecule is termed a corepressor.
    There is also a remarkable feedback system which exists in metabolic chains, preventing overproduction without involving the repressor system at the gene level.  This works by what is called allosteric inhibition of enzymes in the chain.  An end-product molecule from that chain may react with an enzyme at the start or at a key juncture of the chain, causing the enzyme to change its shape.  As a result, it is no longer able to function in its usual capacity as an enzyme catalyst to keep the chain going.⁸

“Ribosomes” Which Process the RNA Copy

   When the mRNA copy of a gene or of an operon is made, the work has only begun, just as when the office staff of an industrial plant makes copies of the blueprints at the request of a shop foreman.  The instructions must then be read and put into action at the cell’s assembly lines.  The correct amino acids must be brought in proper order and fastened together to form the needed protein chain.
    We may picture the next key figure as a production foreman with a complex assembly machine.  He arranges for various workers to read the copy of the instructions and to bring the items in proper order so the foreman can link them together, using the machinery which he has on hand for that purpose.
    In the cell, this key figure is known as a ribosome (pronounced rye-bo-sohm).  It fulfills the job just described—of the foreman with the assembly machinery.  A ribosome is a very small object made of proteins and RNA.  It looks somewhat like a volleyball pressed against a basketball.  As to purpose,

This particle coordinates the translation of the genetic information in the sequence of the nucleotide bases in the messenger RNA (transcribed from the DNA molecule, the gene) to the sequence of amino acids in each protein manufactured in the cell.¹⁰

Transfer RNA, Delivery Vehicle for Amino Acids

    While the mRNA is being processed by the ribosome in order to assemble amino acids into a protein, how will these amino acids actually be brought into the proper order?  There does not seem to be any innate attraction or affinity between an amino acid and the RNA letters which code for it.
    In the early research after the Watson-Crick breakthrough, it became apparent that there must be intermediates to bring the amino acids to the ribosome in proper order.  Two such vital go-betweens were finally located.  One serves as a transport molecule.  It is called transfer-RNA, which is a different form of RNA from that which has been described.  Transfer-RNA, written tRNA, is a comparatively short chain of RNA containing some seventy-five or eighty ribonucleotides.  The RNA strand doubles back on itself, and base-pairs with its own chain in some places.  The overall shape of the tRNA molecule in some ways resembles a key or a cloverleaf.  If tRNA is to do its job properly, the shape must be very precise, and this seems to depend in part upon the right temperature and the correct concentration of certain ions (e.g., magnesium and sodium) in the cell fluid.
    Transfer-RNA is perfectly fitted for its mission.  First of all, each tRNA type attaches to only one variety of the twenty amino acids.  Secondly, the particular tRNA delivers that amino acid in the proper sequence for the forming protein.  This is possible because the tRNA molecule has at one end a special RNA triplet of code letters which match the mRNA codon which specifies that particular amino acid.  When these complementary codons come together by base-pairing, the amino acid being transported by that tRNA is thus in position to be linked to the growing protein chain in the correct order.  All this takes place at the ribosome, which is like a mobile assembly machine as it moves along the mRNA strand (or as the mRNA tape passes through the ribosomes).

There must be enough tRNA species to match each of the twenty types of amino acids.  Further, there ought to be enough to read each of the sixty-one codons which signify amino acid types.  Recent research is filling in the gaps in this direction.  In fact, there are indications that there may be more than enough to equal the number of codons.¹²  There is one instance known where two different kinds of tRNA are used for the same codon, but for a special reason.  One of these two serves only to initiate a protein chain—in bacteria, where it has been found.¹³  A tRNA may read multiple codons (wobble theory).

The Enzyme “Interpreter”

The second intermediate which is involved in bringing amino acids for proper assembly is perhaps even more vital.  There seems to be no natural attraction between an amino acid and its own transfer-RNA, so something must bring them together.  It is as if there were two languages, and neither party understands the other except when there is an interpreter to bridge the gap.  This essential task is done by a special group of enzymes which match the different tRNA’s and amino acids.  One part of each such enzyme fits just its own particular kind of amino acid and no other.  Another part of the enzyme interacts with its own type of tRNA.  In plain language, it can be pictured as follows: the enzyme grasps its amino acid and its tRNA and fastens them together.¹⁴

Summarizing the Translation Process

Connecting all the parts of the protein-forming complex into an abbreviated simple description, we begin with DNA which is the master original containing the instructions for cell activities.  When there is need, parts of the DNA instructions are copied and sent out into the cell in the form of messenger-RNA.

This mRNA tape then passes through one or more ribosomes which “read” the coded instructions with the aid of transfer-RNA molecules which bring the particular amino acids called

    To anyone with an interest in biology, the protein synthesizing mechanism which has been described is fascinatingly intriguing.  One can hardly wait for further experiments that may explain gaps in present knowledge.  As research continues, the plan of cell operation becomes more amazing than ever.
    For one example, in 1969 biochemists at the Weizmann Institute of Science in Israel reported that multiple special enzymes are required to bind the messenger-RNA to the ribosome before protein synthesis can begin.  They called attention to “the complexity of this scheme . . . the mechanism which ensures correct protein chain initiation, and, thereby, accurate translation of the genetic code.”¹⁵
    Further, two other researchers gave evidence that one or more special proteins are also involved in protein termination.¹⁶
    Furthermore, many other special factors are involved during the main process of protein synthesis.  These include an enzyme

for binding the tRNA to the ribosome at its first or “A” position, and another “transfer factor” to move this tRNA to the second or “P” position.  Between these two events, the vital joining of the forming chain onto the new amino acid by the formation of the peptide bond is brought about at the “A” position by a special enzyme which apparently exists in only one copy per ribosome and is part of the larger (50-8) ribosome particle.  Magnesium, GTP (similar to ATP), and several other agents are found to be involved also in protein formation.  Much of the process remains to be clarified, but the above gives some idea of the picture as it seems to date.

Highly Organized Efficiency in an Intricate System

    It becomes increasingly clear what a highly integrated, complex, effective system is involved in living things.  This is true in the simplest known living cell, as well as in cells of the human body.  In scientific literature one encounters the highest praise of this marvelous system by some of the scientists who know it best.
    Atomic physicist George Gamow was involved in attempts to solve the DNA code after the first Watson-Crick breakthrough.  He even obtained the help of two cryptologists who were government experts at solving secret codes.  Gamow waxed eloquent over what he called in popular terminology “gene molecules”:

    Indeed, considering on the one hand the remarkable permanence of genes, which carry almost without any deviation the properties of a given species through thousands of generations, and, on the other hand the comparatively small number of individual atoms that form one gene, one cannot consider it otherwise than as a well-planned structure in which each atom or atomic group sits in its predetermined place.¹⁷

of a base sequence.”¹⁸  At the conclusion of his book, Molecules and Evolution, he waxed religious in the manner of a dedicated materialist.  Jukes seems to make DNA his object of worship, expressing the following poetic sentiment in prose form.  After crediting evolution (by random changes and natural selection) for the development of life to the present stage, he said:

MAN: Five hundred million years ago, a billion years ago, the long molecules were joined together in the pools of tepid water.
    Phosphate, sugar; phosphate, sugar, phosphate; A, C, T, and G; C, A, G, and T. . . .
   (Five hundred million years, a billion years, the long rods, immortally never-changing, mortally ever-changing, reached the day, when, through what they had wrought, they saw themselves as in a mirror.)¹⁹

    How did this amazing system come to be?  The only answers which an evolutionist has are vague and unsatisfying when examined closely.  Crick did the best he could with the problem, considering that he clearly did not want to acknowledge any supernatural element being involved.  Here is his explanation:

    It is the next steps that seem difficult, and that may not be easy to study.  At the moment when natural selection started, was there only nucleic acid and no protein?  Or, on the other hand, was there only protein and no nucleic acid?  The difficulty of these alternatives is that if we had protein alone it is not easy to think of a simple replication process, whereas if we had nucleic acid alone (which would make the replication easy) it is difficult to see how nucleic acid could provide the necessary catalytic activity.  A third possibility, which to my mind is rather promising, is that when natural selection began both nucleic acid and protein existed, and that the synthesis of protein was crudely coupled to nucleic acid in the same sort of way as it is today.  At first sight it seems highly unlikely that this complicated mechanism could have arisen by chance, but it is really quite possible that some primitive version of it started in that way and although not perfect was sufficiently accurate to enable the system to get going.
    The real difficulty about the origin of life is that the experimental evidence showing what happened has long ago

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152               Evolution: Possible or Impossible?

disappeared.  All we are left with is a certain amount of frozen history in the organisms as we see them today.  This is going to make it scientifically very difficult, because it is inevitable that there will be more theories than there are facts to disprove them.²⁰

None of the parts of an airplane can fly by itself.  Only the whole airplane can fly.  An airplane, it seems, is a bunch of non-flying parts organized to fly. . . .
    None of the molecular parts of a living cell can live by itself.  Only the whole cell can live.  A living cell, it seems, is a bunch of non-living molecules organized to live.
    Organization, not substance, seems to make the difference between life and non-life.²²

    Professor Parker explains the reason why life could not have started spontaneously, whether one considers proteins first or DNA first, or both.

    There’s one thing protein molecules can’t do: reproduce.  Reproduction is the function of DNA.  DNA can reproduce itself.  ..and DNA can reproduce proteins. . . .
    DNA, however, can neither reproduce itself accurately nor make protein without a host of helpers, including several

already existing protein molecules.  So, life really depends upon the relationship between DNA and protein-DNA (or related nucleic acid) for reproduction and protein for structure and function.  This DNA-protein relationship is basic to life in viruses and all known life forms.²³

we will again use the smaller theoretical “minimal living system” resulting from Morowitz’ research for the National Aeronautics and Space Administration.
    When we remember that chance strains itself in making over five trillion attempts in order to spell “evolution” once, it seems almost ludicrous even to proceed in asking whether such amazing items as the DNA code could have started by chance.  The odds against a gene sequence will be too astounding to comprehend.