DNA - DeoxyriboNucleic Acid
DNA - Digital Network Architecture [DEC]
"DNA can be considered to be biological nanosoftware; ribosomes, large scale molecular constructors. Enzymes are what Nature chose as truly functional molecular sized assemblers. Genetic engineers are not creating new tools per se, but rather, adapting and improvising from what Nature has already provided. Future generations of engineers, armed with molecular engineering techniques, will have a real chance of imitating and perhaps improving on Nature."
- _Imitating The Molecular Workings of Nature_
"Other intelligent monkeys have walked this planet.
We exterminated them and so now we are unique, but what is loose on this planet
systems that reflect functions of DNA: learning, coding, templating, recording,
testing, retesting, recoding against DNA functions. Then again, language
may be a quality of an entirely different order. Whatever language is,
it is in us monkeys now and moving through us and moving out of our hands and
into the noosphere
with which we have surrounded ourselves."
-Terence McKenna - _Archaic Revival_
The individualist must fulfill his or her genetic predisposition to be a pioneer, and the only way one can do that today is by moving into space faster than anything else. I think the maverick Seed is included in the DNA scenario to serve that function in each epoch. I'm leaving Earth for the same reason my ancestors left Europe: freedom is found on the expanding, pioneering perimeter, never inside the centralized state. To quote another Zen koan, "Where is the Tao?" "Move on!"
Anton Wilson - _The Illuminati
As we now know, since the discovery
of DNA, we arise out of sequences of what are called codons, which are the nucleotide
units in the DNA which code for protein. The messenger RNA takes the template
of the DNA and runs itself through a ribosome, and the ribosome gathers amino
acids out of the ambient
environment, connecting them up to create a protein. What this means is that
we are, in fact, textual. Each one of us is a word of approximately 700,000,000
characters, and this word is made flesh when the sperm and the egg form a zygote
and the DNA textural message is downloaded into matter. Now we are on the brink
of decoding the human genome, and the end result of this is that the flesh will
be made word.
- Terence McKenna - _Timewave Zero And Language_
or deoxyribonucleic acid, NUCLEIC ACID found in the nuclei of CELLS. It
is the principal constituent of GENES (linear segments of DNA) and CHROMOSOMES,
the structures that transmit hereditary characteristics. The amount of
DNA is constant for all typical cells of any given species of plant or
animal, regardless of the size or function of that cell. Each DNA molecule
is a long, two-stranded chain made up of subunits, called nucleotides,
containing a sugar (deoxyribose), a phosphate group, and one of four nitrogenous
bases: adenine (A), guanine (G), thymine (T), and cytosine (C). In 1953
J.D. WATSON and F.H. CRICK proposed that the strands, connected by hydrogen
bonds between the bases, were coiled in a double helix. Adenine bonds only
with thymine (A-T or T-A) and guanine only with cytosine (G-C or C-G).
The complementarity of this bonding insures that DNA can be replicated,
i.e., that identical copies can be made in order to transmit genetic information
to the next generation.
The transcription enzymes read only the parts of the DNA text that code for the construction of proteins and enzymes. These passages, called "genes," represent only 3 percent of the human genome, according to various estimates. The remaining 97 percent are not read; their function is unknown.
Scientists have found spread out among the non-coding
parts of the text a great number of endlessly repeated sequences with no
apparent meaning, and even palindromes,
which are words or sentences that can be read in either direction.
They have called this apparent gibberish, which constitutes the overwhelming
majority of the genome, "junk DNA."
- _Cosmic Serpent: DNA And The Origins Of Knowledge_ by Jeremy Narby p. 100
Palindrome - "...and we saw a Jawa sew DNA"
Shamans say the correct way to talk about spirits is in metaphors. Biologists confirm this notion by using a precise array of anthropocentric and technological metaphors to describe DNA, proteins, and enzymes. DNA is a text, or a program, or data, containing information, which is read and transcribed into messenger-RNA's. The latter feed into ribosomes, which are molecular computers that translate the instructions according to the genetic code. They build the rest of the cell's machinery, namely the proteins and enzymes, which are miniaturized robots that construct and maintain the cell. - p. 137
|Sugar (sucrose)||Sugar (deoxyribose)||
track _Phenomena_ MP3
off of _Phenomena_ 12"x3
on Koyote (1996)
samples: "Intelligent life beyond this planet.";
"A small group from S.E.T.I.
- search for extra terrestial intelligence - used
a radio dish at Arecibo
to send out a message to whoever might be listening. They sent about a quarter
of a kilobyte including structure of human DNA, a map of our solar system, population
of the earth, helpful facts like that."
Deoxyribonucleic acid (DNA) is the primary chemical component of chromosomes and is the material of which genes are made. It is sometimes called the "molecule of heredity," because parents transmit copied portions of their own DNA to offspring during reproduction, and because they propagate their traits by doing so.
In bacteria and other simple cell organisms, DNA is distributed more or less throughout the cell. In the complex cells that make up plants, animals and in other multi-celled organisms, most of the DNA resides in the cell nucleus. The energy generating organelles known as chloroplasts and mitochondria also carry DNA, as do many viruses.
Overview of molecular structure
Although sometimes called "the molecule of heredity," pieces of DNA as people typically think of them are not single molecules. Rather, they are pairs of molecules, which entwine like vines to form a double helix.
Each vine-like molecule is a strand of DNA: a chemically linked chain of nucleotides, each of which consists of a sugar, a phosphate and one of four kinds of aromatic "bases." Because DNA strands are composed of these nucleotide subunits, they are polymers.
The diversity of the bases means that there are four kinds of nucleotides, which are commonly referred to by the identity of their bases. These are adenine (A), thymine (T), cytosine (C), and guanine (G).
In a DNA double helix, two polynucleotide strands come together through complementary pairing of the bases, which occurs by hydrogen bonding. Each base forms hydrogen bonds readily to only one other -- A to T and C to G -- so that the identity of the base on one strand dictates what base must face it on the opposing strand. Thus the entire nucleotide sequence of each strand is complementary to that of the other, and when separated, each may act as a template with which to replicate the other.
Because pairing causes the nucleotide bases to face the helical axis, the sugar and phosphate groups of the nucleotides run along the outside, and the two chains they form are sometimes called the "backbones" of the helix. In fact, it is chemical bonds between the phosphates and the sugars that link one nucleotide to the next in the DNA strand.
Mechanical properties relevant to biology
Because hydrogen bonds are weak compared to covalent bonds, the strands of the double helix can be easily separated by enzymes or even, as in PCR, by gentle heating. On the other hand, gentle heating works only on pieces of DNA that are less than about 10,000 base pairs (10 kilobase pairs, or 10 kbp) long. The intertwining of the DNA strands makes long segments difficult to separate. Enzymes known as helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase. The unwinding requires that helicases chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other.
When the ends of a piece of double-helical DNA are joined so that it forms a circle, as in plasmid DNA, the strands are topologically knotted. This means they cannot be separated by gentle heating or by any process that does not involve breaking a strand. The task of unknotting topologically linked strands of DNA falls to enzymes known as topoisomerases. Some of these enzymes unknot circular DNA by cleaving two strands so that another double-stranded segment can pass through. Unknotting is required for the replication of circular DNA as well as for various types of recombination in linear DNA.
Space-filling model of a section of DNA molecule
The DNA helix can assume one of three slightly different geometries, of which the "B" form described by James Watson and Francis Crick is believed to predominate in cells. It is 2 nanometers wide and extends 3.4 nanometers per 10 bp of sequence. This is also the approximate length of sequence in which the helix makes one complete turn about its axis. This frequency of twist (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbors in the chain.
The narrow breadth of the double helix makes it impossible to detect by conventional electron microscopy, except by heavy staining. At the same time, the DNA found in many cells can be macroscopic in length -- approximately 5 centimeters long for strands in a human chromosome. Consequently, cells must compact or "package" DNA to carry it within them. This is one of the functions of the chromosomes, which contain spool-like proteins known as histones, around which DNA winds.
The B form of the DNA helix twists 360° per 10.6 bp in the absence of strain. But many molecular biological processes can induce strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoiled". DNA in vivo is typically negatively supercoiled, which facilitates the unwinding of the double-helix required for RNA transcription.
The two other known double-helical forms of DNA, called A and Z, differ modestly in their geometry and dimensions. The A form appears likely to occur only in dehydrated samples of DNA, such those used in crystallography experiments, and possibly in hybrid pairings of DNA and RNA strands. Segments of DNA that cells have methylated for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis like a mirror image of the B form.
The role of the sequence
Within a gene, the sequence of nucleotides along a DNA strand defines a protein, which an organism is liable to manufacture or "express" at one or several points in its life using the information of the sequence. The relationship between the nucleotide sequence and the amino-acid sequence of the protein is determined by simple cellular rules of translation, known collectively as the genetic code. Reading along the "protein-coding" sequence of a gene, each successive sequence of three nucleotides (called a codon) specifies or "encodes" one amino acid.
In many species of organism, only a small fraction of the total sequence of the genome appears to encode protein. The function of the rest is a matter of speculation. It is known that certain nucleotide sequences specify affinity for DNA binding proteins, which play a wide variety of vital roles, in particular through control of replication and transcription. These sequences are frequently called regulatory sequences, and researchers assume that so far they have identified only a tiny fraction of the total that exist. "Junk DNA" represents sequences that do not yet appear to contain genes or to have a function.
Sequence also determines a DNA segment's susceptibility to cleavage by restriction enzymes, the quintessential tools of genetic engineering. The position of cleavage sites throughout an individual's genome determines one kind of an individual's "DNA fingerprint".
DNA sequence reading
The asymmetric shape and linkage of nucleotides means that a DNA strand always has a discernable orientation or directionality. Because of this directionality, close inspection of a double helix reveals that, although the nucleotides along one strand are heading one way (e.g. the "ascending strand") the others are heading the other (e.g. the "descending strand"). This arrangement of the strands is called antiparallel.
For reasons of chemical nomenclature, people who work with DNA refer to the asymmetric termini of each strand as the 5' and 3' ends (pronounced "five prime" and "three prime"). DNA workers and enzymes alike always read nucleotide sequences in the "5' to 3' direction". In a vertically oriented double helix, the 3' strand is said to be ascending while the 5' strand is said to be descending.
As a result of their antiparallel arrangement and the sequence-reading preferences of enzymes, even if both strands carried identical instead of complementary sequences, cells could properly translate only one of them. The other strand a cell can only read backwards. Molecular biologists call a sequence "sense" if it is translated or translatable, and they call its complement "antisense". It follows then, somewhat paradoxically, that the template for transcription is the antisense strand. The resulting transcript is an RNA replica of the sense strand and is itself sense.
Some viruses blur the distinction between sense and antisense, because certain sequences of their genomes do double duty, encoding one protein when read 5' to 3' along one strand, and a second protein when read in the opposite direction along the other strand. As a result, the genomes of these viruses are unusually compact for the number of genes they contain, which biologists view as an adaptation.
Topologists like to note that the juxtaposition of the 3' end of one DNA strand beside the 5' end of the other at both termini of a double-helical segment makes the arrangement a "crab canon".
More on DNA replication
...DNA replication...origin of replication...chromosome...plasmid...DNA polymerase...mutation...
Single-stranded DNA and repair of mutations
In some viruses DNA appears in a non-helical, single-stranded form. Because many of the DNA repair mechanisms of cells work only on paired bases, viruses that carry single-stranded DNA genomes mutate more frequently than they would otherwise. As a result, such species may adapt more rapidly to avoid extinction. The result would not be so favorable in more complicated and more slowly replicating organisms, however, which may explain why only viruses carry single-stranded DNA. These viruses presumably also benefit from the lower cost of replicating one strand versus two.
The discovery of DNA and the double helix
Working in the 19th century, biochemists initially isolated DNA and RNA together from cell nuclei. They were relatively quick to appreciate the polymeric nature of their "nucleic acid" isolates, but realized only later that nucleotides were of two types--one containing ribose and the other deoxyribose. It was this subsequent discovery that led to the identification and naming of DNA as a substance distinct from RNA. Not until 1943 did Oswald Theodore Avery provide the first compelling evidence that DNA could carry genetic information.
How it could do so was unimaginable at the time. Because chemical dissection of DNA samples always yielded the same four nucleotides, the chemical composition of DNA appeared simple, perhaps even uniform. Organisms, on the other hand, are fantastically complex individually and widely diverse collectively. Geneticists did not speak of genes as conveyors of "information" in such words, but if they had, they would not have hesitated to quantify the amount of information that genes need to convey as vast. The idea that information might reside in a chemical in the same way that it exists in text--as a finite alphabet of letters arranged in a sequence of unlimited length--had not yet been conceived. It would emerge upon the discovery of DNA's structure, but few researchers imagined that DNA's structure had much to say about genetics.
In the 1950s, only a few groups made it their goal to determine the structure of DNA. These included an American group led by Linus Pauling, and two in Britain. At Cambridge University, Crick and Watson were building physical models using metal rods and balls, in which they incorporated the known chemical structures of the nucleotides, as well as the known position of the linkages joining one nucleotide to the next along the polymer. At King's College, London, Maurice Wilkins and Rosalind Franklin were examining x-ray diffraction patterns of DNA fibers.
A key inspiration in the work of all of these teams was the discovery in 1948 by Pauling that many proteins included helical shapes. Pauling had deduced this structure from x-ray patterns. Even in the initial crude diffraction data from DNA, it was evident that the structure involved helices. But this insight was only a beginning. There remained the questions of how many strands came together, whether this number was the same for every helix, whether the bases pointed toward the helical axis or away, and ultimately what were the explicit angles and coordinates of all the bonds and atoms. Such questions motivated the modeling efforts of Watson and Crick.
In their modeling, Watson and Crick restricted themselves to what they saw as chemically and biologically reasonable. Still, the breadth of possibilities was very wide. A breakthrough occurred in 1952, when Erwin Chargaff visited Cambridge and inspired Crick with a description of experiments Chargaff had published in 1947. Chargaff had observed that the proportions of the four nucleotides vary between one DNA sample and the next, but that for particular pairs of nucleotides--adenine and thymine, guanine and cytosine -- the two nucleotides are always present in equal proportions.
Watson and Crick had begun to contemplate double helical arrangements, and they saw that by reversing the directionality of one strand with respect to the other, they could provide an explanation for Chargaff's puzzling finding. This explanation was the complementary pairing of the bases, which also had the effect of ensuring that the distance between the phosphate chains did not vary along a sequence. Watson and Crick were able to discern that this distance was constant and to measure its exact value of 2 nanometers from an X-ray pattern obtained by Franklin. The same pattern also gave them the 3.4 nanometer-per-10 bp "pitch" of the helix. The pair quickly converged upon a model, which they announced before Franklin herself published any of her work.
The great assistance Watson and Crick derived from Franklin's data has become a subject of controversy, and it has angered people who believe Franklin has not received the credit due to her. The most controversial aspect is that Franklin's critical X-ray pattern was shown to Watson and Crick without Franklin's knowledge or permission. Wilkins showed it to them at his lab while Franklin was away.
Watson and Crick's model attracted great interest immediately upon its presentation. Arriving at their conclusion on February 21, 1953, Watson and Crick made their first announcement on February 28. Their paper 'A Structure for Deoxyribose Nucleic Acid' was published on April 25. In an influential presentation in 1957, Crick laid out the "Central Dogma", which foretold the relationship between DNA, RNA, and proteins, and articulated the "sequence hypothesis." A critical confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 in the form of the Meselson-Stahl experiment. Work by Crick and coworkers deciphered the genetic code not long afterward. These findings represent the birth of molecular biology.
Watson, Crick, and Wilkins were awarded a Nobel Prize in 1962, by which time Franklin had died.