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The deoxyribose molecule occupies the center position in the nucleotide, flanked by a phosphate group on one side and a base on the other. The phosphate group of each nucleotide is also linked to the deoxyribose of the adjacent nucleotide in the chain. These linked deoxyribose-phosphate subunits form the parallel side rails of the ladder. The bases face inward toward each other, forming the rungs of the ladder.

The nucleotides in one DNA strand have a specific association with the corresponding nucleotides in the other DNA strand. Because of the chemical affinity of the bases, nucleotides containing adenine are always paired with nucleotides containing thymine, and nucleotides containing cytosine are always paired with nucleotides containing guanine. The complementary bases are joined to each other by weak chemical bonds called hydrogen bonds.
In 1953 American biochemist James D. Watson and British biophysicist Francis Crick published the first description of the structure of DNA. Their model proved to be so important for the understanding of protein synthesis, DNA replication, and mutation that they were awarded the 1962 Nobel Prize for physiology or medicine for their work.
DNA carries the instructions for the production of proteins. A protein is composed of smaller molecules called amino acids, and the structure and function of the protein is determined by the sequence of its amino acids. The sequence of amino acids, in turn, is determined by the sequence of nucleotide bases in the DNA. A sequence of three nucleotide bases, called a triplet, is the genetic code word, or codon, that specifies a particular amino acid. For instance, the triplet GAC (guanine, adenine, and cytosine) is the codon for the amino acid leucine, and the triplet CAG (cytosine, adenine, and guanine) is the codon for the amino acid valine. A protein consisting of 100 amino acids is thus encoded by a DNA segment consisting of 300 nucleotides. Of the two polynucleotide chains that form a DNA molecule, only one strand, called the sense strand, contains the information needed for the production of a given amino acid sequence. The other strand aids in replication.

Protein synthesis begins with the separation of a DNA molecule into two strands. In a process called transcription, a section of the sense strand acts as a template, or pattern, to produce a new strand called messenger RNA (mRNA). The mRNA leaves the cell nucleus and attaches to the ribosomes, specialized cellular structures that are the sites of protein synthesis. Amino acids are carried to the ribosomes by another type of RNA, called transfer RNA (tRNA). In a process called translation, the amino acids are linked together in a particular sequence, dictated by the mRNA, to form a protein.
A gene is a sequence of DNA nucleotides that specify the order of amino acids in a protein via an intermediary mRNA molecule. Substituting one DNA nucleotide with another containing a different base causes all descendant cells or viruses to have the altered nucleotide base sequence. As a result of the substitution, the sequence of amino acids in the resulting protein may also be changed. Such a change in a DNA molecule is called a mutation. Most mutations are the result of errors in the replication process. Exposure of a cell or virus to radiation or to certain chemicals increases the likelihood of mutations.

In most cellular organisms, replication of a DNA molecule takes place in the cell nucleus and occurs just before the cell divides. Replication begins with the separation of the two polynucleotide chains, each of which then acts as a template for the assembly of a new complementary chain. As the old chains separate, each nucleotide in the two chains attracts a complementary nucleotide that has been formed earlier by the cell. The nucleotides are joined to one another by hydrogen bonds to form the rungs of a new DNA molecule. As the complementary nucleotides are fitted into place, an enzyme called DNA polymerase links them together by bonding the phosphate group of one nucleotide to the sugar molecule of the adjacent nucleotide, forming the side rail of the new DNA molecule. This process continues until a new polynucleotide chain has been formed alongside the old one, forming a new double-helix molecule.

Several tools and procedures facilitate are used by scientists for the study and manipulation of DNA. Specialized enzymes, called restriction enzymes, found in bacteria act like molecular scissors to cut the phosphate backbones of DNA molecules at specific base sequences. Strands of DNA that have been cut with restriction enzymes are left with single-stranded tails that are called sticky ends, because they can easily realign with tails from certain other DNA fragments. Scientists take advantage of restriction enzymes and the sticky ends generated by these enzymes to carry out recombinant DNA technology, or genetic engineering.

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