User talk:Thomas Wright Sulcer/sandbox7

Temporary file: Intron; (possible suggestions for new material March 5, 2010)

When DNA makes a protein, introns are spliced off during this process, so only the exons remain.

An intron is the intervening, non-coding sequence of nucleic acid that is between the expressed sequences (exons) in a gene. It is removed from the primary RNA transcript by splicing and is a common feature of eucaryotic genes. Introns are the spacer regions of DNA that separate the information-coding parts of a gene.

Generally introns are found in the DNA of more advanced species. Scientists believe that the only living creatures on earth billions of years ago were bacteria which belonged to a group called prokaryotes. But about two billion years ago, a group branched off from prokaryotes called eukaryotes which evolved into much more complex organisms including animals, plants, fungi, and some protozoans, and which had bigger and more complex DNA. A New York Times science reporter explains:

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The eukaryote genome is downright baroque. It is typically much bigger and carries many more genes. Eukaryotes can do more with their genes, too. They can switch genes on and off in complex patterns to control where and when they make proteins. And they can make many proteins from a single gene.

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Why is the DNA more advanced? It's segmented. The DNA alternates between what are called exons and introns. This allows human cells to "edit out introns" when copying genes to build proteins, and lets cells make a wide variety of different proteins from the same gene. It is believed that the exons were functionless stretches whose only purpose was to break up stretches of exons, but this view has been questioned. Scientist Michael Lynch suspected the addition of introns into DNA was a harmful accident at first. When an intron was wedged into the middle of a gene, cells had to be able to recognize the boundaries and "skip over" the introns when making a protein. Lynch hypothesized that this first led to defective proteins, but that the overall effect of interspersed introns was a phenomenon called genetic drift which ultimately helped evolution, since it created new opportunities for adaptations to be successful.

There is no single mechanism for splicing an intron from the primary RNA transcript. Introns are classified into four groups based on the mechanism of splicing. In general splicing can be either autocatalytic or be catalyzed by a large complex of proteins know as the spliceosome. Splicing can also be viewed as a form of gene regulation since alternative splicing can result in different combinations of exons in the mature RNA transcript. In this way one gene can code for distinct open reading frames and hence has the potential to code for more than one protein.

The human DNA helix, if unraveled, would be about three feet long, and the sections of introns inside it have been referred to as "mostly chaotic" and an "indecipherable wilderness".

Sometimes the DNA that codes for introns is classified as junk DNA but this is an oversimplification since introns can contain functional RNA or DNA sequences; these include transfer RNA (tRNA) or microRNA (miRNA) sequences. In the chromosome, DNA sequences that code for an intron can also include enhancers that are important for gene expression.

The true role of introns is unclear but one hypothesis is that introns allow gene shuffling to occur, resulting in the creation of new exon combinations and novel proteins. The presence of an intron can also enhance gene expression since the process of RNA splicing seems to facilitate the trafficking of the mRNA out of the eucaryotic nucleus.

Discoveries

After completing the human genome in 2001, scientists found 22,000 genes, but noticed there were more than 100,000 different proteins. If each gene could make only one protein, then how could there be so many different proteins? A Washington Post reporter explained:

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When a gene is activated, it is first transcribed into an intermediate molecule called mRNA. The introns are clipped out and the exons spliced together, and the whole thing is then translated into the protein. Biologists used to think one gene produced one protein. Now it's clear that one gene can produce many different proteins. Under certain conditions, a cell clips out not only the intron fillers but also one or more of the exons. This is like taking a speech and removing many of the sentences. Done in different ways, it can produce many different messages.

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Scientists think that about five percent of the human genome has a "message" of one sort or another, with a particular order of nucleotide letters (A, G, C, T) being of utmost importance in determining important aspects of a human's body chemistry. Any addition, deletion, or change can have a big effect, including death. Still, there are large stretches of genes which had been thought to have been "junk DNA" but is turning out to have an important role. These conserved "non-coding elements" include insulators, micro-RNAs, exon-splicing enhancers, e'-untranslated hairpins and other molecules which are "emerging from the shadows." They regulate the activity of genes that do make the proteins by turning them on and off, tweaking them, and coordinating the sequential action of their effects. And how these processes operate are important not only for geneticists, but for scientists who study evolution, since "more of evolution's survival-of-the-fittest battles occurred in writing the instruction manual for running the genes than in designing the genes themselves," according to a Washington Post report in 2007.

The naming of intron

The names intron and exon were described as "less catchy" but nevertheless "novel" names, and the naming was against a trend of using "dull and pedantic" impenetrable Latin names. In 1977, three scientists at a cafeteria in Basel, Switzerland, discussed possible names. Dr. Walter Gilbert was credited for thinking up the name intron, while Dr. Melvin Cohn coined the term exon, although he was originally thinking of the large oil firm Exxon. Dr. Cohn explained:

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I was actually thinking of 'exxon' with two x's like the oil company -- it was a joke -- I was making fun of Gilbert because I didn't think those were the best possible terms. They were too slangy and didn't best describe what was going on.

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Nevertheless, Dr. Gilbert wrote down the terms on a napkin, and both terms appeared in a 1978 commentary in the journal Nature.

Recent research involving introns

According to one source, scientists are exploring ways of using data from introns when doing DNA analysis regarding police investigations. While each intron seems chaotic, there are repetitive sequences of the genetic alphabet sometimes called "stutters" or "burps" which can be analyzed. When multiple probes are used, it's possible to analyze introns in the DNA to identify its uniqueness and produce an identification "as reliable as a human fingerprint."

Scientists discovered that two DNA units that switch off the lactase gene are in "the 9th and 13th introns of a neighboring gene whose role strangely has nothing to do with lactose metabolism." Scientists are discovering that the spacer-regions in DNA called introns "play unexpected roles in gene control."

Researchers are studying the relationship between introns and gender-related differences in colon cancer.

There are suggestions that the composition of a specific intron, a three-SNP haplotype in the intron 1 of OCA2, is related to "human eye color variation", and scientists believe two major genes and several minor ones which account for the "tremendous variation in human eye color."

There was speculation that introns inside the dysbindin gene may have a role in schizophrenia.