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  CHAPTER 8:  DNA: The Most Golden of All Molecules

Page 125

   Chapter 8

DNA — “The Most Golden of All Molecules”


In terms of an analogy, [human DNA is like] a very large
encyclopaedia of forty-six volumes, 20,000 pages each.
Every cell in the human body is provided with the whole

—John C. Kendrew

THE GREATEST DISCOVERY in the history of biology was that of the structure of DNA.  It captured the imagination of the general public, particularly those already interested in science.2  Understanding it is a key part of our progress to certainty.
    That there should be a “language of life,” as Crick called it,3 which is a universal code, is very mysterious and intriguing.  The code has been found to be precisely the same in the cells of the smallest known living thing and in the nerve cells of the human brain.  Yeast cells and the eye-retina cells of an eagle contain the exact same code with identical letters, arranged to spell different “words.”  Abundant research indicates this universal nature of the code to be the same in all creatures studied (with possibly very rare minor variations).

Size of the DNA Molecule

DNA, like protein, is a long slender thread in its primary structure. In fact, a DNA molecule may be hundreds of times

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as long as the diameter of the cell of which it is a part.  This requires it to be doubled up and coiled or twisted around so it can fit into the cell.
    A multicelled plant or animal will have more DNA per cell, since more coded information is needed.  In the human cell, the DNA is divided into 46 chromosomes.  The total length of all this DNA in one cell is about six feet!4  It is estimated that the total DNA content in your body would span the solar system!5

A Quick Way to Understand the Plan of the Code

    We can get a clear idea of how the DNA code is arranged by designing one of our own.  Suppose we form a code in which only four symbols are to be used, the numerals 1, 2, 3, and 4.  It is to be translated later into the 26 letters of our alphabet.
    If we decide to put the numerals in groups of three, then we will have more than enough triplets of digits to match the 26 letters.  In fact, we will have 64 different trios (111, 112, 113, 114, 121, 122, etc.).  Because of the excess of these trios as compared to 26 letters, we can assign several different groups of three to the same letter, in most cases.
    Let’s let the letter “A” be coded by any of the following groups of digits, 111, 112, 113, 114.  “B” can be represented by 121, 122, 123, or 124. For “C,” we will assign only two triplets, 131 and 132.  This will give us enough for the moment.
    Now, using our simple code, let’s write the word “Cab.”  It could possibly be 132114122.6  To translate it, all we need do is divide it into groups of three, beginning at the correct starting point.  Then, by referring to our code key or dictionary, we can easily decipher it.
    It would work just the same if other symbols were used instead of the numerals 1, 2, 3, 4.  For example, we could use a circle, a square, a triangle, and an oval.  We could, as another alternative, use four different types of tree leaves, or even four chemicals.  In the latter case, our code would be much like the DNA code, as we will see.  DNA, however, does not translate to our alphabet but to the 20 amino acids, indicating the proper order for their joining, to make a specific protein that is needed.  Biological life consists, to a great extent, of making the correct

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proteins with the proper timing and amounts.7  Once formed, these various proteins can do many wonderful things.
    Now that we have the main idea of the code plan, let’s examine the way it actually exists in living things.

The Exotic DNA “Double Helix”

    Watson and Crick and their co-workers discovered that this marvelous deoxyribonucleic acid molecule (DNA) consisted of a special type of spiral, a double helix.  The long molecule continuously winds like the threads of a screw.  Together the two sides of the double helix form a spiral staircase or ladder.  (See Figures 5 and 6.)
    When studying proteins, we found that a protein molecule is formed from smaller amino acid molecules, of which there are 20 kinds.  DNA is likewise made of simpler molecules, but there are only six kinds.  Four of these carry the message and the other two protect and hold them in place.

The above diagram depicts a short section of the DNA molecule in flattened form to show the ladderlike sides with steps or rungs consisting of the four “bases” which are the letters of the genetic code.  Each base is connected to another by hydrogen bonds in the center of the ladder, thus forming a “base pair.”  The letters A, C, G, and T are the first initials of the four bases: adenine, cytosine, guanine, and thymine.  In the sides of the ladder, the round molecules are phosphates, and the pentagonal ones are sugar molecules.  Diagram is from same source as Fig. 6.  See next page.

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Shown above schematically is the DNA double helix in its natural coiled configuration.  This is primarily to show the twisting of the ladder, and does not show the base pairing except to list letters of complementary bases in triplets or codons.  In an actual DNA molecule, there are ten base pairs for each complete corkscrew turn of the double helix.

From “The Genetic Code: II” by Marshall W. Nirenberg.  Copyright © March, 1963, by Scientific American, Inc.  All rights reserved.  Dr. Nirenberg’s important work led to deciphering the genetic code.



The coiled representation shown here is drawn more closely to scale than are the two preceding diagrams.  This shows a section of the DNA molecule containing about one hundred base pairs or letters.  The bases almost completely fill the space between the coiled sides of the twisted ladderlike double helix.  This small section would be less than a ten-thousandth as long as the complete DNA molecule of a bacterium if drawn to the same scale.  This picture is by Francis H. C. Crick, codiscoverer of the DNA structure.

From “The Genetic Code,” by F. H. C. Crick.  Copyright © October, 1962, by Scientific American, Inc.  All rights reserved.

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The four chemical bases which serve as letters of DNA.  Figures 8 and 9 are from same source, given after Figure 9 on following page.
    First, let’s consider the sides of the staircase or spiral ladder.  Each side is quite simple.  It consists of only two kinds of molecules, alternating in regular fashion.  One is a type of sugar, called deoxyribose (the D in DNA).  The other component of the ladder’s sides is a small molecule called a phosphate.  It contains one atom of phosphorus, along with oxygen atoms.  These two kinds of molecules join together in a very long chain —sugar-phosphate-sugar-phosphate-sugar— in regular order.  The entire length of each side of the DNA double spiral is formed on this simple plan.  These sides of the ladder may be thought of as frames to hold the letters in place.
    The rungs or steps of the ladder are the all-important “letters” of the language of life.  These are nitrogen compounds which
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Schematic picture of base pairing in the DNA double helix.  Dotted lines represent hydrogen bonds.

    Figures 8 and 9 are adapted from “How Cells Make Molecules” by Vincent G. Allfrey and Alfred E. Mirsky.  Copyright © September, 1961, by Scientific American, Inc.  All rights reserved.

DNA—“The Most Golden of All Molecules”                131

also contain oxygen, hydrogen, and carbon.  There are four kinds of these in DNA.  They are called bases.
    A base is joined to each sugar molecule of the sides of the ladder.  Each base extends halfway across to the other side of the helical ladder and connects with another base which is similarly projecting from the opposite side of the ladder.  Together the two bases make a base pair.  They can be pictured as steps of the spiral ladder.
    These four bases are the all-important symbols or letters of the code.  The names of the bases are: adenine, guanine, thymine, and cytosine.  (In biochemistry, usually names which end with “-ine” are pronounced as if spelled “-een”; thus, adenine is pronounced “adeneen.”)
    A base pair consists of two different bases, joined together loosely by hydrogen bonds where they meet in the middle of the helix.  Adenine always pairs with thymine, and guanine pairs only with cytosine, in DNA.
    Watson and Crick discovered this complementary pairing mechanism of the bases.  By this discovery, if you know what base is on one side of the spiral, you will know also the base that connects with it.  Just a certain one will pair with it to complete that base pair.  Using initial letters of the four bases, we say that “A” always pairs with “T,” and “G” always pairs with “C.”
A single base with its own section of one side of the ladder makes up a complete unit called a nucleotide.  It consists of a base, a deoxyribose sugar molecule, and a phosphate.  A base pair with its sections of both sides of the ladder is a nucleotide pair.  A nucleotide pair has more than 60 atoms.  “The exact order of these pairs constitutes a genetic message which contains all the information necessary to determine the specific structures and functions of the cell.”8
    This completes a look at the building blocks that form the DNA double helix.

Letters of the Universal Language

    The all-important part of the DNA helix consists of the letters or bases that make up the code.  Just as in our language the order of the letters spells out an endless variety of messages, so with DNA.  Abbreviated as above, these letters are A, C, G, and T.

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Courtesy of Dr. Arthur Kornberg.  All rights reserved.

Shown above are three DNA molecules.  In the two “circular” molecules, the long slender thread of DNA is connected in the form of a loop, which is the normal situation in bacteria and viruses.  The molecules shown contain perhaps 5,000 base pairs or code letters, which is quite short for DNA.  (The DNA molecule of a bacterium may be a thousand times as long, and would be difficult to show in one picture.)
    The electron micrograph above depicts double-stranded DNA formed in a famous experiment by Arthur Kornberg of Stanford University, and for which he is a Nobel laureate.  It consists of synthetic double-stranded DNA, obtained by first making a hybrid of one strand from a bacterial virus and a synthetic strand formed by base pairing with this pattern strand.  Activated nucleotides which are the precursors or building blocks of DNA and an enzyme(s) produced by living bacteria were used.  Each thread in the picture is actually a double helix ladderlike chain, too small to see in detail even at the high magnification shown (around 78,700 diameters).

DNA—“The Most Golden of All Molecules”                133

It is their order in the chain that carries the message, just as the order of letters in this line of type carries the thought.
    Each base always has the same complementary base opposite it.  In a sense, this might seem to narrow down the number of letters to only two if the base pairs could be read from either side.  From research to date, it seems that the code is read from only one side of the double helix.  That one side carries the message to be transcribed, and the other is called the “nonsense” side.  There are, therefore, four letters instead of two in the usable alphabet.  (The so-called “nonsense” side has at least two very important functions, as we will see, making possible the replication or duplicating process, and also enabling the cell to repair injured DNA.)

Changing From Four Letters to Sixty-four “Triplets”

    At first thought it might seem impossible for only four symbols to carry much variety in messages.  The DNA system solves this in the same manner as our code using the four numerals.  The symbols of the code are read in groups of three.  Each triplet of bases is called a codon.  This system, employing only four letters to be read in groups of three is a marvelously simple plan.  Intelligence sometimes combines simple things to get complex results.
    Always DNA appears to be read three letters at a time, in the same direction, without overlapping.  The reading must begin from a certain starting point, of course.
    The code in the double helix has no divisions between these triplets.  If we print it as translated into these four initials, it might look like this, for a certain section of DNA: AGTCAAGCAGGGTCTCCC.  As can be seen, it is important to know where to start so that the reading of the triplet codons will be in correct frame.

Translating to Proteins

    Through long, patient investigation, biochemists figured out which codon, or trio, is translated into which amino acid in making a protein chain.  It was found that in many instances several different triplets are assigned to the same amino acid.  Three of the 64 codons indicate “end of chain.”  These serve as punctuation to signal the completion of a protein.
    Research is still going on as to whether there are reasons for more than one codon to indicate the same amino acid.  There

134               Evolution: Possible or Impossible?

are four such codons that code for glycine, for example.  Hints are being discovered that there is good reason for having several.9  Duplicate codons are thought to have something to do with the rate or speed of making proteins.  Some amino acids are coded by as many as six different codons—each of which translates into the same amino acid as the others.  On the other hand, the amino acid methionine has only one codon, as does tryptophan.  Duplicates may be “a regulatory factor in some cases.”10

How DNA Duplicates Itself

    Let us now quite briefly consider the amazing process of the replication of DNA itself.  This is the vital process on which all heredity depends.  It is reproduction at the molecular level.  Without this DNA copy-making process, life could not be passed along with continuity, if at all.
    Francis Crick a few years ago described a preliminary problem:

There are still a number of things about the process we do not understand, not the least of which is the fact that the two chains are not lying side by side, but are wound round one another, and that in order for the replication to take place they must be at some stage unwound In addition, the process appears to be one of great precision.11
    Those who have examined electron micrographs of DNA have noticed the coiled, doubled, knotted twisting and turning that, from our point of observation, appear common in DNA molecules.  Anyone who has ever tried to untangle a microphone cord or lamp cord will wonder how on earth the DNA thread ever can manage this intricate feat.  It must progressively divide, making two double-helix chains in place of one along the entire length of the molecule.  The DNA, remember, is much longer than the diameter of the cell, sometimes about a thousand times as long!12  Ideas on how the unwinding may occur
135               Evolution: Possible or Impossible?

by rotation as the replication proceeds are feverishly under study.  In fact, it is reported that the rotation during this unwinding occurs at the rate of more than seventy-five turns per second per growing point in bacteria.
    Pictures have been taken of the DNA molecule of the smallest living thing, to which we have referred before, the Mycoplasma hominis H39.  This DNA is in the form of a long threadlike molecule, joined together in a circle.  Actual replication in process was photographed by H. R.  Bode and Harold Morowitz at Yale.13
    The molecule begins dividing into two threads at a certain point, and the division apparently continues until there are two circular loops of DNA instead of one.  These then separate and become the DNA for two daughter cells.  This is an unbelievable “miracle” when you look at the seeming tangles of the long thread during the duplicating process.  Somehow it happens successfully, with a built-in wisdom which at this stage we cannot fathom.  The mechanism involves a growing point complex, containing special proteins and possibly RNA.  This complex may be attached to the cell membrane.

Complementary Pairing Is the Secret of Replication

    The replication process seems to work in this way.  When the two strands begin to split apart, this leaves each half of the ladder separate.  (See Figure 11.)  Each “base” is thus left with no partner.
    Floating around in the “juice,” there are various cell parts which have already been made on instructions from the DNA.  These free-floating parts include nucleotides, ready to be fitted together to form a strand of the DNA spiral.  The nucleotides are in an activated condition, with extra phosphates added to give them energy for uniting.
    From the multitude of free-floating nucleotides, the correct matching ones come alongside the divided strands of the DNA which is duplicating.  As we recall, each base will match none but its one-and-only opposite type.  These then link up to the existing strand and to each other, with the aid of enzymes.  When the process is completed, the DNA is again a ladderlike, double helix.  Each half of the original is replicating at the same

DNA—“The Most Golden of All Molecules”                136



DNA replication or duplication takes place when the ladder-like double helix divides down the center and a new strand forms alongside each of the divided halves, thus making two complete ladders.  By the rules of base pairing, the new strand in each case will be identical to the side it replaces.  The nucleotide units from which it is assembled are preformed and available in activated form in the cell.  The linking is done by enzymes at a very rapid rate, in opposite directions on the two strands-continuously on one and perhaps in short sections on the other near the fork.

From “The Synthesis of DNA” by Arthur Kornberg.  Copyright © October, 1968, by Scientific American, Inc.  All rights reserved.

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time.  Each finally becomes a complete double spiral.  Complementary pairing insures that it will be identical to the original.
    This is the secret of heredity.  This is the ingenious method by which like begets like, and life is passed on to the next generation with continuity and exactness.  We still scarcely realize how greatly everything depends on DNA, the only means of duplicating life.
    While joined, the two sides of the helix protect the bases between them.  When replicating, each half can make a complementary copy.  That is why there are two sides instead of one.14  When Watson discovered this, he said it was “too pretty not to be true.”15  It has been described as “this exquisite capability of nucleic acids to direct their own replication.”16  This duplication is so accurate that it would correspond to a rate of error of less than one letter in an entire set of the Encyclopaedia Britannica.17

Summarizing the Language of Life

Since we have had to get rather technical, let’s pause and summarize the code and its message.  The letters A, C, G, and T are strung along the spiral DNA thread.  The letters are read three at a time.  Each triplet or codon of letters tells which amino acid is to be placed next in order in arranging a protein molecule.  Three of these codons are assigned as punctuation to indicate “end chain.”     This marvelously simple code is the language of life.  Thomas H. Jukes in his monumental work Molecules and Evolution tells about one type of special protein (cytochrome c) which is common to all forms of life except some of the simplest.  In cytochrome c, the order of letters is the same for certain parts of the chain in all species which have been examined.  We will

DNA—“The Most Golden of All Molecules”                138

look into this in chapter 12. He concludes that these “could scarcely have persisted for several hundred million years unless the code remained unchanged and identical in all the species involved.”18
    Many other biologists have commented on this astounding fact that the DNA code appears to be universal, the same language in every creature on earth, whether virus, elephant, or pine tree.19
    In all earthly life, “the sequence of these nucleotides constitutes the set of instructions for the biochemical machinery of the cell.”20
    Before we go on to see how this intriguing language is translated through a very exact and beautiful process, it may be helpful to pause and reflect.

A Language Indicates an Intelligent Source

Let us consider this question: By all the rules of reason, could there be a code which carries a message without someone originating that code?  It would seem self-evident that any such complex message system, which is seen to be wise and effective, requires not only an intelligence but a person back of it.
    Who wrote the DNA code?  Who is the author of this precise language?  There is no evolutionary explanation that even begins to be an adequate answer.  Professor Carl R. Woese put the situation frankly when he wrote, “We have to be content with a few naive conjectures to fill in the great gap of the code’s evolution.”21
    The only logical thing to do is to listen to the voice of reason and to acknowledge that only God, the infinite Person, could author that amazing living language!

  1 John C. Kendrew, The Thread of Life (Cambridge, Mass.: Harvard University Press, 1966), p. 104.

  2 Codiscoverer Watson, as noted earlier, termed this fascinating chemical “the most golden of all molecules!”

  3 1969 Yearbook of Science and the Future (Britannica), p. 123.

  4 Philip Handler, ed., Biology and the Future of Man (New York: Oxford University Press, 1970), p. 134.

  5 Kendrew, The Thread of Life, p. 63.

  6 We could, of course, have used any of the alternates, when more than one group stands for a particular letter.

  7 Handler, ed. Biology and the Future of Man, p. 146.

  8 Roger Y. Stanier, Michael Doudoroff, and Edward A. Adelberg, The Microbial World, 3rd ed.  (Englewood Cliffs, N.J.: Prentice-Hall, 1970), p. 267.

  9 James Kan, Marshall W. Nirenberg, and Noboru Sueoka, “Coding Specificity of Escherichia coli Leucine Transfer Ribonucleic Acids,” Journal of Molecular Biology, Vol.  52 (1970), pp. 179-193.  Also:
   Joseph Ilan, “The Role of tRNA in Translational Control of Specific mRNA during Insect Metamorphosis,” Symposia on Quantitative Biology (Cold Spring Harbor Laboratory, Long Island, N.Y., 1969), Vol. XXXIV, pp. 787-791.

  10 Marshall W. Nirenberg, National Institutes of Health, personal telephone conversation, October, 1971.

  11 Francis H. C. Crick, Of Molecules and Men (Seattle: University of Washington Press, 1966), pp. 39, 40.

  12 lbid., p. 37.

  13 Hans R. Bode and Harold J. Morowitz, “Size and Structure of the Mycoplasma hominis H39 Chromosome,” Journal of Molecular Biology, Vol. 23 (1967), p.198.

  14 It also allows an ingenious repair mechanism if one side is damaged, as we intimated earlier.  (Philip C. Hanawalt and Robert H. Haynes, “The Repair of DNA,” Scientific American, Vol. 216 [February 1967], pp. 36-43).  This procedure is so complex that some scientists now believe that at least four different genes are required to control just the first step.  (Akira Taketo et al., “Initial Step of Excision Repair in Escherichia coli,” Journal of Molecular Biology, Vol. 70, No. 1 [September 14, 1972], pp. 1-14).

  15 James D. Watson, The Double Helix (New York: Atheneum Press, 1968), p.210.

  16 Handler, ed., Biology and the Future of Man, pp. 34, 38.

  17 Calculated from the following estimate: “The average probability of an error in the insertion of a new nucleotide under optimal conditions may be as low as 10-8 to 10-9.”  (James Watson, The Molecular Biology of the Gene, 2nd ed., [Menlo Park, Calif.: W. A. Benjamin, Inc., 1970], p. 297.)

  18 Thomas H. Jukes, Molecules and Evolution, (New York: Columbia University Press, 1966), p. 73.

  19 Viruses could not operate successfully if it were otherwise.  The code words in a virus give orders to the “host cell” which it has invaded.  These coded instructions are carried out in the same way as if the host had given the same order with its DNA.  (In passing, we might note that viruses may be one result of the curse brought upon the world by sin, as described in Genesis 3:17, 18.  This was intimated briefly in an earlier chapter.)

  20 Handler, ed., Biology and the Future of Man, p. 32.

  21Carl R. Woese, “The Biological Significance of the Genetic Code,” Progress in Molecular and Subcellular Biology, ed. F. E. Hahn (New York: Springer-Verlag, 1969), p. 27.


Chapter 7 Table of Contents Chapter 9