The INDIVIDUALIST

A Wiki about biochemical individuality

Genomics

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Description

The chemical inside the nucleus of a cell that carries the genetic instructions for making living organisms.

Discussion

Deoxyribonucleic acid (DNA) is a nucleic acid —usually in the form of a double helix— that contains the genetic instructions specifying the biological development of all cellular forms of life, and most viruses. DNA is a long polymer of nucleotides and encodes the sequence of the amino acid residues in proteins using the genetic code, a triplet code of nucleotides.

In complex Eukaryotic cells such as those from plants, animals, fungi and protists, most of the DNA is located in the cell nucleus. By contrast, in simpler cells called prokaryotes, including the eubacteria and archaea, DNA is not separated from the cytoplasm by a nuclear envelope. The cellular organelles known as chloroplasts and mitochondria also carry DNA.

DNA is often referred to as the molecule of heredity as it is responsible for the genetic propagation of most inherited traits. In humans, these traits can range from hair colour to disease susceptibility. During cell division, DNA is replicated and can be transmitted to offspring during reproduction. Lineage studies can be done based on the facts that the mitochondrial DNA only comes from the mother, and the male Y chromosome only comes from the father.

Every person's DNA, their genome, is inherited from both parents. The mother's [mitochondrial DNA]? together with twenty-three chromosomes from each parent combine to form the genome of a zygote, the fertilized egg. As a result, with certain exceptions such as red blood cells, most human cells contain 23 pairs of chromosomes, together with mitochondrial DNA inherited from the mother.

http://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossary/Illustration/Images/dna.gif

The chemical structure of DNA.

Contrary to a common misconception, the DNA is not a single molecule, but rather a pair of molecules joined by hydrogen bonds: it is organized as two complementary strands, head-to-toe, with the hydrogen bonds between them. Each strand of DNA is a chain of chemical "building blocks", called nucleotides, of which there are four types: adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). (Thymine should not be confused with thiamine, which is vitamin B1.) In some organisms, most notably the PBS1 phage, Uracil (U) replaces T in the organism's DNA.[1] These allowable base components of nucleic acids can be polymerized in any order giving the molecules a high degree of uniqueness.

Between the two strands, each base can only "pair up" with one single predetermined other base: A+T, T+A, C+G and G+C are the only possible combinations; that is, an "A" on one strand of double-stranded DNA will "mate" properly only with a "T" on the other, complementary strand; therefore, naming the bases on the conventionally chosen side of the strand is enough to describe the entire double-strand sequence. Two nucleotides paired together are called a base pair. On rare occasions, wrong pairing can happen, when thymine goes into its enol form or cytosine goes into its imino form. The double-stranded structure of DNA provides a simple mechanism for DNA replication: the DNA double strand is first "unzipped" down the middle, and the "other half" of each new single strand is recreated by exposing each half to a mixture of the four bases. An enzyme makes a new strand by finding the correct base in the mixture and pairing it with the original strand. In this way, the base on the old strand dictates which base will be on the new strand, and the cell ends up with an extra copy of its DNA.

DNA contains the genetic information that is inherited by the offspring of an organism; this information is determined by the sequence of base pairs along its length. A strand of DNA contains genes, areas that regulate genes, and areas that either have no function, or a function yet unknown. Genes can be loosely viewed as the organism's "cookbook" or "blueprint".

Other interesting points:
  • DNA is an acid because of the phosphate groups between each deoxyribose. This is the primary reason why DNA has a negative charge.
  • The "polarity" of each pair is important: A+T is not the same as T+A, just as C+G is not the same as G+C (note that "polarity" as such is never used in this context -- it's just a suggestive way to get the idea across)
  • Mutations are chemical imperfections in this process, where a base is accidentally skipped, inserted, or incorrectly copied, or the chain is trimmed, or added to; many basic mutations can be described as combinations of these accidental "operations". Mutations can also occur through chemical damage (through mutagens), light (UV damage), or through other more complicated gene swapping events.
  • DNA molecules that act as enzymes are known in laboratories, but none have been known to be found in life so far.
  • In addition to the traditionally viewed duplex form of DNA, DNA can also acquire triplex and quadruplex forms. Here instead of the Watson-Crick base pairing, Hoogsten base pairing comes into picture.
  • DNA differs from ribonucleic acid (RNA) by having a sugar 2-deoxyribose instead of ribose in its backbone. This is the basic chemical distinction between RNA and DNA. In addition, in RNA, the nucleotides thymine (T) are replaced by uracil (U).

Molecular structure

http://www.dadamo.com/wiki/dna-rna.png

Comparisons between DNA and single stranded RNA with the diagram of the bases showing.

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 (see the illustration at the right).

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 and C to G -- so that the identity of the base on one strand dictates the strength of the association; the more complementary bases exist, the stronger and longer-lasting the association.

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.

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