Monday, March 30, 2009
Junk DNA
In chapter three, Sean Carroll discusses the structure and layout of DNA, noting the sequences known as introns, or non-coding segments. He refers to these sequences as "junk" DNA, saying that this DNA is merely an accumulation of informationless sequences; as such, he chooses mostly to ignore introns. However, many would protest such an abjection. Having thouroughly studied the mechanisms of DNA in Campbell chapter 17, do you agree with Carroll's assertation? Or, as some scientists now feel, do you believe there is a purpose to these seemingly useless sequences? Explain your opinion.
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"In humans, and many other complex species, genes occupy only a small fraction of all of the DNA, and are separated by long intervals of noncoding DNA. Some of this noncoding DNA functions in the control of how genes are used, but a lot of it is what is called 'junk,'" (Carroll 76). I disagree with Carroll on this point in that introns are "junk DNA." There is a purpose to these seemingly useless sequences otherwise "nature would not go to all that trouble without a reason." I believe that introns have a purpose in evolution - they allow greater genetic recombination between exons. This idea was first suggested in 1978 by Walter Gilbert, of Harvard, which was called "exon shuffling." Introns could promote further recombination which could enhance the amount of diverse species and taxa. I also agree with some other scientists who believe that introns serve functions in shaping alternative splicing (that of exons) and influence the expression of the gene as Carroll stated. "There are also cases in which introns contain genes for small nuclear RNA, which is important for the translation of messenger RNA, an intermediary between DNA and proteins. Nuclear introns can also be important in a process called alternative splicing, which can produce multiple types of messenger RNA from a single gene." This discussion relates to the biological theme of heritable information in the form of DNA - where introns code a majority of the DNA as so called "spacers" between "useful" genetic code.
ReplyDeleteFor further reading and sources:
http://www.sciam.com/article.cfm?id=what-is-known-about-the-f
http://batzerlab.lsu.edu/Hum_Mol_Gen_Lectures/Paper_Critique_Example.pdf
http://www.rae.org/introns.html
There are a large number of scientists, myself included, that reject Carroll's statement that introns are useless.
ReplyDeleteScientists lean towards two opposing theories when it comes to this issue. In the introns-early theory (aka exon theory of genes), scientists theorize that exons are minigenes that used to function as a whole gene in our ancient less complex forms. The theory also explains why less complex organisms like bacteria lack introns. The theory goes on to state that our current genes are the combination of multiple exons, and that introns are used to hold the genes together, and hence were formed along with the creation of genes. The intron-late theory, on the other hand, argues that introns originated to circumvent the problem of the random distribution of stop codons in random primordial sequences, and hence were formed after genes were created.
There must be a reason for why introns exist, because through selective advantage, we would have eventually gotten rid of introns if they didn't have any purpose. However, it is most difficult to pinpoint exactly what the specific purpose of introns are. The aforementioned two theories propose two possible purposes for introns.
I beleive that introns are very important to the genetic code, simply because of the dangerous world in which we live, where mutagens run rampant (mutagens result from smoking, UV rays, and eating free-radical-ridden food). I beleive that introns are used as a mutagen buffer, whereby because there is a lot of non-coding DNA, the chance of a random mutation (such as thymine dymers) occuring in coding DNA is greatly reduced. This in turn decreases the chance of a detrimental mutation occuring in the DNA that reduces fitness and chance of sexual reproduction.
ReplyDeleteI think that Carroll was being a little sarcastic when he termed noncoding sequences in the human genome as the “junk DNA”. In fact, in other section of the book, Carroll couldn’t emphasize enough the importance of junk DNA to biologist in the process of understanding evolution. Junk DNA is only a general term given to any non-coding DNA. However, there are many types of DNA such as introns, SINEs and LINEs, and fossil genes. Chapter 17 of Campbell discusses the importance of introns in RNA processing. During RNA processing, enzymes called spliceosomes excised introns from the pre-mRNA and splice together the exons. However, it is important to note that introns can be coding DNA. A segment of DNA can be an intron in one splicing but an exon in another. The various combinations of introns and exons code a mass number of proteins. This is also the reason why humans can get by with a relatively small number of genes. The number of protein made by the human body greatly outnumbers the number of genes in the human genome. SINEs and LINEs are also import genetic markers on the human genome. SINEs and LINEs are extremely useful to evolutionary biologist who uses SINEs and LINEs to determine the evolutionary relationships between organisms. This is possible because “once a SINE or LINE is inserted, there is no active mechanism for remove it” (Carroll 99). This brings up to the Third theme of biology: heritable information. Junk DNA, along with coding DNA are all genetic information that is passed down from generation to generation and are necessary to maintain the continuity of a species. However the flow of information for DNA is a two way exchange. Because current organisms retain all of the DNA from its ancestors, biologist can trace this genetic information to understand the life of the ancestors of an organism. Junk DNA such as fossil genes is especially useful in this process since it reveals the genes that the ancestors of an organism once had. Since genes reflect the selection pressure from the environment, biologist could study fossilized genes to determine the facts about an organism such as its behavior and the habit. The above examples are more enough to prove the importance of the so called junk DNA. Therefore, the word “junk” shouldn’t be used to characterize DNA that is vastly important to organism and biologist alike.
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