Although sometimes called "the molecule of heredity", DNA macromolecules 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 (deoxyribose),a phosphate and one of five kinds of nucleobases ("bases"). Because DNA strands are composed of these nucleotide subunits, they are polymers.
The diversity of the bases means that there are five kinds of nucleotides, which are commonly referred to by the identity of their bases.
These are adenine (A), thymine (T), uracil (U), cytosine (C), and guanine (G). U is rarely found in DNA except as a result of chemical degradation of C, but in some viruses, notably PBS1 phage DNA, U completely replaces the usual T in its DNA.
Similarly, RNA usually contains U in place of T, but in certain RNAs such as transfer RNA, T is always found in some positions.
Thus, the only true difference between DNA and RNA is the sugar, 2-deoxyribose in DNA and ribose in RNA.
In a DNA double helix, two polynucleotide strands can associate through the hydrophobic effect and pi stacking.
Specificity of which strands stay associated is determined by complementary pairing. Each base forms hydrogen bonds readily to only one other,
A to T forming two hydrogen bonds and C to G forming three hydrogen bonds.
The GC content and length of each DNA molcule dictates the strength of the association; the more complementary bases exist, the stronger and longer-lasting the association characterised by the temperature required to break the hydrogen bonding, its Tm value.
The cell's machinery is capable of melting or disassociating a DNA double helix, and using each DNA strand as a template for synthesizing a new strand which is nearly identical to the previous strand. Errors that occur in the synthesis are known as mutations. The process known as
PCR (polymerase chain reaction) mimics this process in vitro in a nonliving system.
Because pairing causes the nucleotide bases to face the helical axis, the sugar and phosphate groups of the nucleotides run along the outside; 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.
Nucleotide sequence
Within a gene, the sequence of nucleotides along a DNA strand defines a messenger RNA sequence which then defines a protein, that 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.
The genetic code consists of three-letter 'words' (termed a codon) formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).
These codons can then be translated with messenger RNA and then transfer RNA, with a codon corresponding to a particular amino acid.
There are 64 possible codons (4 bases in 3 places 43) that encode 20 amino acids. Most amino acids, therefore, have more than one possible codon.
There are also three 'stop' or 'nonsense' codons signifying the end of the coding region, namely the UAA, UGA and UAG codons.
In many species, only a small fraction of the total sequence of the genome appears to encode protein.
For example, only about 1.5% of the human genome consists of protein-coding exons. 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 tohave a function. The reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size
("C-value") among species represent a long-standing puzzle in DNA research known as the "C-value enigma".
Some DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few (if any) protein-coding genes, but are
important for the function and stability of chromosomes. Some genes code for "RNA genes" (see tRNA and rRNA). Some RNA genes code for transcripts that function as regulatory RNAs (see siRNA) that influence the function of other RNA molecules. The intron-exon structure of some genes
(such as immunoglobin and protocadeherin genes) is important for allowing alternative splicing of pre-mRNA which allows several different proteinsto be made from the same gene. Some non-coding DNA represents pseudogenes, which have been hypothesized to serve as raw genetic material for the
creation of new genes through the process of gene duplication and divergence.
Some non-coding DNA provided hot-spots for duplication of short DNA regions; such sequence duplication has been the major form of genetic change in the human lineage (see evidence from the Chimpanzee Genome Project).
Exons interspersed with introns allows for "exon shuffling" and the creation of modified genes that might have new adaptive functions.
Large amounts of non-coding DNA is probably adaptive in that it provides chromosomal regions where recombination between homologous portions of
chromosomes can take place without disrupting the function of genes. Some biologists such as Stuart Kauffman have speculated that non-coding DNA may modify the rate of evolution of a species.
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".
