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Deoxyribonucleic acid

Synonyms: DNA, thymonucleic acid
German: Desoxyribonukleinsäure, DNS

1 Definition

The deoxyribonucleic acid (DNA) is a very large molecule containing phosphorus and nitrogen, and carries genetic information. Proteins are produced with the help of this information inscribed in the DNA in a specific form, which is termed the genetic code.

2 The structure of DNA

The structure of DNA was deciphered in 1953 by James Watson and Francis Crick, for which achievement they received the Nobel prize in 1962. According to the model of both researchers, the DNA is made of two antiparallel, single DNA strands. Each single strand has one 5' and one 3' end. At the 5' end is located a phosphate residue, and at the 3' end, the OH group.

The DNA has a rope ladder-structure, in which the two side-pieces of the ladder are helically entwined around an imaginary axis (double helix structure). Both side pieces of the rope ladder are made of hundreds of thousands of interchanging sugar (deoxyribose) and phosphate residues, within which each DNA single strand (side piece) is linked to each other by fixed atomic bonds.

The rungs of the rope ladder consist of two organic bases respectively (a so-called base pair), which are bound to each other by hydrogen bonds (weaker bonding forces) and thus ensure that even in helical shape both side pieces remain bound to the rope ladder and at the same distance to each other. In the DNA, there exist four different organic bases: adenine, cytosine, guanine and thymine, usually abbreviated by the letters A, C, G and T. The base pairs are formed by the complementary bases adenine and thymine as well as cytosine and guanine respectively. Two hydrogen bonds develop between adenine and thymine; cytosine and guanine are connected by three hydrogen bonds.

In other words, the giant molecule DNA is "stuck together" by numerous pieces of four different nucleotides, which can be bound to each other in one DNA single strand in arbitrary sequence and differ from each other, so that each of them contain only one of four possible organic bases.

Three such bases, as they directly lie in a row in a single DNA strand, respectively form a so-called base triplet or codon. Each base triplet represents one of 20 amino acids, which form the proteins. The sequence of the bases - and thereby the base triplets – determines the sequence of the amino acids in the proteins. The structure of the proteins within the DNA is described with the help of the base sequence. Initially, the information of the DNA is transcribed to mRNA molecules in the protein biosynthesis. The information transmitted by the mRNA is then translated in the ribosome to a polypeptide chain. (For details, see genetic code).

3 Duplication/replication of DNA

The DNA can duplicate itself with the help of enzymes. It is replicated according to the so-called semi-conservative principle. Initially, the double-stranded helix is unraveled by the enzyme helicase. A single strand is the matrix for the complementary strand to be synthesized, i.e. the replicated DNA consists of one old and one new synthesized complementary single strand. The DNA synthesis, i.e. the binding of the nucleotides to be linked, is carried out by enzymes from the group of DNA polymerases. A nucleotide can only be combined, if it exists as a triphosphate connection – that is, as a deoxyribonucleoside triphosphate. By splitting two phosphates, the energy necessary for the process is released.

In the area of the replikation fork formed by the enzyme helicase (i.e. two diverging DNA single strands), an RNA primer first marks the starting point of the new DNA synthesis. The DNA polymerase then attaches to the RNA-molecule a nucleotide complementary to the old single DNA strand nucleotide, to which it binds another corresponding nucleotide and so on until the DNA has been completed to form another double helix. This takes place on both open single strands.

However, a problem arises: the combination of the new nucleotides to a complementary DNA single strand is only possible in the 5'→3' direction, i.e. continuously along the old 3'→5' strand (and thereby reading it) in the direction of the opening replication fork without any interruption. But, the synthesis of the second new strand on the old 5'→3' strand cannot take place continuously toward the replication fork, but only away from it, as also in the 5'→3' direction. At the beginning of the replication, the replication fork is only slightly open, and therefore only a short piece of new complementary DNA can develop on this strand – all but in 'unsuitable' opposite direction. Since a DNA polymerase combines only approximately 1000 nucleotides here, it is necessary to synthesize the entire complementary strand piece by piece. Once the replication fork is unwound further, a new RNA primer once again binds directly to the DNA single strand at the bifurcation, and the next DNA polymerase begins – away from the replication fork – to bind approximately 1000 nucleotides to the RNA primer. The same process is repeated again, i.e. the complementary DNA strand is formed in fragments. In the synthesis of the 3'→5' strand, a new RNA primer is required for each DNA synthesis unit. The primer and the corresponding synthesis unit are called Okazaki fragment.

It should be noted that the RNA primer required for the start of the replication are enzymatically metabolized. This creates gaps in the new DNA strand, which are filled with DNA nucleotides by special DNA polymerases. Eventually, the enzyme ligase combines the new DNA fragments not yet linked together to form a single, long, complementary single strand.

After the replication is completed, two single DNA strands are supplemented in slightly differing ways to form another double strand respectively. Thus, one DNA molecule becomes two.

4 Other functions of the DNA

Mutations of DNA segments, e.g. exchange of bases with others or changes in the base sequence, lead to alterations of the genetic material, which can be partly lethal for the concerned organism. Sometimes, such mutations can also be advantageous; they form the starting point for the change of living creatures in the scope of evolution. DNA molecules also play a role as carriers of information and "docking station" for enzymes, which account for the transcription. See RNA polymerase. Furthermore, the information of certain DNA segments, as found in operative units like the operon, are important for regulatory processes within the cell.

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