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DNA (deoxyribonucleic acid)

DNA Double Helix

DNA Double Helix: A Recent Discovery of Enormous Complexity
The DNA Double Helix is one of the greatest scientific discoveries of all time. First described by James Watson and Francis Crick in 1953, DNA is the famous molecule of genetics that establishes each organism's physical characteristics. It wasn't until mid-2001, that the Human Genome Project and Celera Genomics jointly presented the true nature and complexity of the digital code inherent in DNA. We now understand that each human DNA molecule is comprised of chemical bases arranged in approximately 3 billion precise sequences. Even the DNA molecule for the single-celled bacterium, E. coli, contains enough information to fill all the books in any of the world's largest libraries.

DNA Double Helix: The "Basics"
DNA (deoxyribonucleic acid) is a double-stranded molecule that is twisted into a helix like a spiral staircase. Each strand is comprised of a sugar-phosphate backbone and numerous base chemicals attached in pairs. The four bases that make up the stairs in the spiraling staircase are adenine (A), thymine (T), cytosine (C) and guanine (G). These stairs act as the "letters" in the genetic alphabet, combining into complex sequences to form the words, sentences and paragraphs that act as instructions to guide the formation and functioning of the host cell. Maybe even more appropriately, the A, T, C and G in the genetic code of the DNA molecule can be compared to the "0" and "1" in the binary code of computer software. Like software to a computer, the DNA code is a genetic language that communicates information to the organic cell.

The DNA code, like a floppy disk of binary code, is quite simple in its basic paired structure. However, it's the sequencing and functioning of that code that's enormously complex. Through recent technologies like x-ray crystallography, we now know that the cell is not a "blob of protoplasm", but rather a microscopic marvel that is more complex than the space shuttle. The cell is very complicated, using vast numbers of phenomenally precise DNA instructions to control its every function.

Although DNA code is remarkably complex, it's the information translation system connected to that code that really baffles science. Like any language, letters and words mean nothing outside the language convention used to give those letters and words meaning. This is modern information theory at its core. A simple binary example of information theory is the "Midnight Ride of Paul Revere." In that famous story, Mr. Revere asks a friend to put one light in the window of the North Church if the British came by land, and two lights if they came by sea. Without a shared language convention between Paul Revere and his friend, that simple communication effort would mean nothing. Well, take that simple example and multiply by a factor containing many zeros.

We now know that the DNA molecule is an intricate message system. To claim that DNA arose by random material forces is to say that information can arise by random material forces. Many scientists argue that the chemical building blocks of the DNA molecule can be explained by natural evolutionary processes. However, they must realize that the material base of a message is completely independent of the information transmitted. Thus, the chemical building blocks have nothing to do with the origin of the complex message. As a simple illustration, the information content of the clause "nature was designed" has nothing to do with the writing material used, whether ink, paint, chalk or crayon. In fact, the clause can be written in binary code, Morse code or smoke signals, but the message remains the same, independent of the medium. There is obviously no relationship between the information and the material base used to transmit it. Some current theories argue that self-organizing properties within the base chemicals themselves created the information in the first DNA molecule. Others argue that external self-organizing forces created the first DNA molecule. However, all of these theories must hold to the illogical conclusion that the material used to transmit the information also produced the information itself. Contrary to the current theories of evolutionary scientists, the information contained within the genetic code must be entirely independent of the chemical makeup of the DNA molecule.

DNA Double Helix: Its Existence Alone Defeats any Theory of Evolution
The scientific reality of the DNA double helix can single-handedly defeat any theory that assumes life arose from non-life through materialistic forces. Evolution theory has convinced many people that the design in our world is merely "apparent" -- just the result of random, natural processes. However, with the discovery, mapping and sequencing of the DNA molecule, we now understand that organic life is based on vastly complex information code, and such information cannot be created or interpreted without a Master Designer at the cosmic keyboard.

DNA Replication

DNA Replication – A brief overview
DNA replication is the basis for biological inheritance. It is a fundamental process occurring in all living organisms to copy their DNA. This process is ‘semiconservative’ in that each strand of the original double-stranded DNA molecule serves as a template for the reproduction of the complementary strand. Hence, the process of DNA replication yields two identical DNA molecules from a single double-stranded molecule. Cellular proof-reading and error-checking mechanisms ensure nearly perfect fidelity of the DNA copies. DNA replication commences at specific locations in the genome called “origins.” The DNA unwinds at the origin to form a replication fork.

DNA replication can proceed in only one direction, from the top of the DNA strand to the bottom. Because the strands that form the DNA double helix align in an antiparallel fashion with the top of one strand juxtaposed to the bottom of the other strand, only one strand at each replication fork has the proper orientation (bottom-to-top) to direct the assembly of a new strand in the top-to-bottom direction. For this leading strand, DNA replication proceeds continuously in the direction of the advancing replication fork.

DNA replication cannot proceed along the lagging strand, i.e. the strand with the top-to-bottom orientation, until the replication bubble expands enough to expose a sizeable stretch of DNA. DNA replication then moves away from the advancing replication fork. It can proceed only a short distance along the ‘top-to-bottom’ oriented strand before the replication process must stop and wait for more of the parent DNA strand to be unwound.

DNA Replication – The Replisome
The replisome is a complex molecular machine that carries out replication of DNA. It is comprised of a number of subcomponents, each performing a specific function during the process of replication. Helicase is an enzyme which breaks the hydrogen bonds between the two strands of DNA, thus separating the strands ahead of DNA synthesis. As helicase unwinds the double helix, it induces the formation of supercoils in other areas of the DNA.

Gyrase relaxes and undoes the supercoiling which has been caused by the helicase by cutting the DNA strands, allowing it to rotate and release the supercoil, and then rejoining the strands. Gyrase is most commonly located upstreak of the replication fork -- where the supercoils are being formed.

Primase adds complementary RNA primers to a DNA strand to begin Okazaki fragments. In addition, because DNA Polymerae can only continue (but not begin) a strand, Primase begins the leading strand as well.

DNA polymerase III is comprised of two catalytic cores -- one for replication of the leading strand and one for the lagging strand. DNA polemerase III, however, cannot stay on the DNA strand long enough to efficiently replicate a daughter strand. Hence, DNA polymerase III stays on the strands via a dimer beta clamp which contains three subunits that come together to enclose the strand -- ensuring that DNA polymerase III will remain on the strand for a few thousand nucleotides as opposed to a few hundred.

DNA polymerase I removes the RNA primers set by Primase and completes the Okazaki fragments. Because there is such a small gap remaining after the action of DNA polymerase I has continued the strand of the Okazaki fragment, ligase is required to fill in the gap. The two ends of the Okazaki fragments are subsequently connected by covalent bonds.

Single-strand binding proteins bind to the exposed bases in an effort to counteract their instability and prevent the single-strand DNA from hydrogen-bonding to itself to form dangerous hairpin structures.

DNA polymerases contain a ‘proofreading’ mechanism, commonly referred to as ‘exonuclease activity’. This removes nucleotides that have been mistakenly added.

DNA Replication – Signature of Design
DNA Replication stands as a fundamental challenge to those who seek to hold to a Darwinian worldview. As the process by which biological information is copied and passed on to succeeding generations, the mechanism is fundamental to the process of self-replication of cells. Yet self-replication of cells is necessary for the operation of any selective process such as natural selection. Thus, to attempt to explain the immense sophistication of this mechanism with reference to natural selection requires one to presuppose the existence of the very thing they wish to explain. Because of its extremely sophisticated nature, most biochemists previously reckoned that the system arose once, prior to the origin of the last universal common ancestor. In addition, many biochemists have long regarded the close functional similarity of DNA replication observed in all life as evidence for the single origin of DNA replication. Yet in 1999 researchers from the National Institutes of Health demonstrated that the core enzymes involved in the DNA replication machinery of bacteria and archae/eukaryotes (the two major trunks of the evolutionary tree of life) did not in fact share a common evolutionary origin. It thus appears as if two identical DNA replication systems have emerged independently in bacteria and archae -- after these two evolutionary lineages supposedly diverged from the last universal common ancestor.

It is phenomenal to think that this engineering marvel evolved a single time, let alone twice. There exists no obvious reason for DNA replication to take place by a semiconservative, RNA primer-dependent, bidirectional mechanism that depends on leading and lagging strands to produce DNA daughter molecules. Even if DNA replication could have evolved independently on two separate occasions, it is reasonable to expect that fundamentally different mechanisms would emerge for bacteria and the archae/eukaryotes given their idiosyncrasies. But, they did not.

DNA structure

DNA structure – An overview
The DNA structure consists of two chainlike molecules (polynucleotides) that twist around each other to form the classic double-helix. The cell’s machinery forms polynucleotide chains by linking together four nucleotides. The nucleotides which are used to build DNA chains are adenosine (A), guanosine (G), cytidine (C), and thymidine (T). DNA houses the information required to make all the polypeptides used by the cell. The sequence of nucleotides in DNA strands (called a ‘gene’) specifies the sequence of amino acids in polypeptide chains.

Clearly a one-to-one relationship cannot exist between the four nucleotides of the DNA structure and the twenty amino acids used to assemble polypeptides. The cell therefore uses groupings of three nucleotides (called ‘codons’) to specify twenty different amino acids. Each codon specifies an amino acid.

Because some codons are redundant, the amino acid sequence for a given polypeptide chain can be specified by several different nucleotide sequences. In fact, research has confirmed that the cell does not randomly make use of redundant codons to specify a particular amino acid in a polypeptide chain. Rather, there appears to be a delicate rationale behind codon usage in genes.

DNA structure – Fine-tuning and optimization
Highly repetitive nucleotide sequences lack stability and mutate readily. However, a study involving the genomes of different organisms at the University of California suggests that codon usage in genes is actually designed to avoid the type of repetition that leads to unstable sequences! Further research indicates that codon usage in genes is also set up to maximize the accuracy of protein synthesis at the ribosome.

Furthermore, the components which comprise the nucleotides also appear to have been carefully chosen in view of enhanced performance. Nucleotides that form the strands of the DNA structure are complex molecules which consist of both a phosphate moiety and a nucleobase (adenine, guanine, cytosine or thymine) joined to a five-carbon sugar (deoxyribose). In RNA, the five-carbon sugar ribose replaces deoxyribose.

The phosphate group of one nucleotide links to the deoxyribose unit of another to form the backbone of the DNA strand. The nucleobases form the ‘ladder rungs’ when the two strands align and twist to form the classical double-helix structure.

Scientists have long known that a myriad of sugars and numerous other nucleobases could have conceivably become part of the cell’s information storage medium (DNA). But why do the nucleotide subunits of DNA and RNA consist of those particular components? Phosphates can form bonds with two sugars simultaneously (called phosphodiester bonds) to bridge two nucleotides, while retaining a negative charge. This makes this chemical group perfectly suited to form a stable backbone for the DNA molecule. Other compounds can form bonds between two sugars but are not able to retain a negative charge. The negative charge on the phosphate group imparts the DNA backbone with stability, thus giving it protection from cleavage by reactive water molecules. Furthermore, the intrinsic nature of the phosphodiester bonds is also finely-tuned. For instance, the phophodiester linkage that bridges the ribose sugar of RNA could involve the 5’ OH of one ribose molecule with either the 2’ OH or 3’ OH of the adjacent ribose molecule. RNA exclusively makes use of 5’ to 3’ bonding. As it turns out, the 5’ to 3’ linkages impart far greater stability to the RNA molecule than does the 5’ to 2’ bonds.

Why do deoxyribose and ribose serve as the backbone constituents of DNA and RNA respectively? Both are five-carbon sugars which form five-membered rings. It is possible to make DNA analogues using a wide range of different sugars that contain four, five and six carbons that can form five- and six-membered rings. But these DNA variants possess undesirable properties as compared to DNA and RNA. For instance, some DNA analogues do not form double helices. Others do, but the nucleotide strands either interact too tightly or too weakly, or they display inappropriate selectivity in their associations. Furthermore, DNA analogues made from sugars that form 6-membered rings adopt too many structural conformations. In this event, it becomes exceptionally difficult for the cell’s machinery to properly execute DNA replication and transcription. Other research shows that deoxyribose uniquely provides the necessary space within the backbone region of the double helix of DNA to accommodate the large nucleobases. No other sugar fulfils this requirement.

DNA structure – Conclusion
The molecular constituents of the DNA structure appear to have optimized chemical properties to produce a stable helical structure capable of storing the information required for the cell’s operation. Detailed accounts of how such an optimized structure for the cell’s most fundamental information storage medium could have arisen naturally have not been produced. To suppose that such extensive optimization could have come into being by blind chance is a far greater leap of faith than many would be willing to take.