Tuesday, December 13, 2011
Chapter 12 Helpful Hints!
This video clearly described the processed of transcription and translation. The video includes the history and experimentation leading to the scientific community discovering the processes of transcription and translation. When the processes are described and explained, there are pictures and diagrams clearly labeling what is happening at each step.
This video shows the process of translation in 3D! I like this video because narrator clearly describes what is occurring at each step during translation. When necessary, the video is stopped and a still picture is shown with labels pointing out all of the pertinent structures. Since this video is the advanced version of mRNA translation, it did not leave out any structures or processes that simpler videos might have left out.
Introns Are There Because...
It is well-known that many eukaryotic pre-mRNA molecules have both introns and exons. The introns are removed from the mRNA, the exons are connected, and then the gene is expressed. A common question has passed through the minds of many. What exactly is the point of introns? What is their function? This article helps to answer these questions.
Introns have been called "junk DNA" but the fact that they are so prevalent and and have been preserved during evolution leads researchers to believe that introns serve some function.
Ashok Bidwai, an assistant professor in the department of biology at West Virginia University, explained how it is widely believed that introns are remnants of genetic sequences that once served as spacers between the stretches of DNA that coded for specific, simpler proteins. As complex proteins were being evolved, regions of the genetic code (domains) may have been shuffled and brought together to generate new sequences that code for protein structures that took on new functions. This hypothesis is based on the observation that the relative positions of introns in genes remain largely the same in organisms from Drosophila melanogaster (the fruit fly) to Caenorhabditis elegans(a widely studied nematode) to mice and humans.
Some researchers have proposed that introns serve as a mechanism that selects for genes that will be expressed early during the development of an organism. There has not been much experimentation to support this hypothesis so its plausibility is uncertain.
Sandro J. de Souza, who works in Walter Gilbert's laboratory at Harvard University, expanded on the prevailing intron hypothesis. There are at least five different types of introns. Some are ribozymes. Some of these ribozymes can splice themselves out of the original transcript. The most common type of intron is called a spliceosomal or nuclear intron.This type of intron is the one found in the nuclear genes of humans.
Generally, nuclear introns are ubiquitous in complex eukaryotes. However, simple prokaryotes and eukaryotes lack introns. In complex multicellular organisms, introns are about ten times longer than the exons. The sequence and length of introns vary rapidly over evolutionary time.
Introns do sometimes have identifiable functions. Scientists have found examples of "functional nuclear introns" that can accommodate sequences important for the expression of the gene on which the intron resides. This function is not a common feature of introns, though. There are also cases in which introns contain genes for small nuclear RNA. Nuclear introns can also be important in alternative splicing, which produces multiple types of messenger RNA from a single gene. Although these examples demonstrate roles for introns, they do not explain why introns are so ubiquitous in our genes.
Introns have been called "junk DNA" but the fact that they are so prevalent and and have been preserved during evolution leads researchers to believe that introns serve some function.
Some researchers have proposed that introns serve as a mechanism that selects for genes that will be expressed early during the development of an organism. There has not been much experimentation to support this hypothesis so its plausibility is uncertain.
Sandro J. de Souza, who works in Walter Gilbert's laboratory at Harvard University, expanded on the prevailing intron hypothesis. There are at least five different types of introns. Some are ribozymes. Some of these ribozymes can splice themselves out of the original transcript. The most common type of intron is called a spliceosomal or nuclear intron.This type of intron is the one found in the nuclear genes of humans.
Generally, nuclear introns are ubiquitous in complex eukaryotes. However, simple prokaryotes and eukaryotes lack introns. In complex multicellular organisms, introns are about ten times longer than the exons. The sequence and length of introns vary rapidly over evolutionary time.
Introns do sometimes have identifiable functions. Scientists have found examples of "functional nuclear introns" that can accommodate sequences important for the expression of the gene on which the intron resides. This function is not a common feature of introns, though. There are also cases in which introns contain genes for small nuclear RNA. Nuclear introns can also be important in alternative splicing, which produces multiple types of messenger RNA from a single gene. Although these examples demonstrate roles for introns, they do not explain why introns are so ubiquitous in our genes.
Bacterial Prolyl-tRNA Synthetase
So this article talks about a specific feature of bacterial prolyl-tRNA synthetase. The article explains how the substrate specificity of bacterial prolyl-tRNA synthetase's editing domain is controlled by a tunable hydrophobic pocket. Aminoacyl-tRNA synthetases are catalysts that covalently attach amino acids onto their respective tRNA's. High accuracy in this reaction is essential to the proper decoding of genetic information for if a charged tRNA molecule contains the wrong amino acid, the incorrect amino acid will be added to the polypeptide chain, thus making a faulty protein. One way the cell tries to prevent this mishap is by proofreading newly synthesized aminoacyl-tRNA molecules. Prolyl-tRNA synthetase (ProRS) mischarges tRNA(Pro) with alanine or cysteine because of their smaller or similar sizes relative to cognate proline. Mischarged Ala-tRNA(Pro) is hydrolyzed by the editing domain, INS, present in most bacterial ProRSs. On the other hand, the INS domain is unable to deacylate Cys-tRNA(Pro). Cys-tRNA(Pro) is hydrolyzed exclusively by a free-standing trans editing domain known as YbaK.
Researchers used computational and experimental approaches to probe the molecular basis of INS domain alanine specificity. In Escherichia coli ProRS, the methyl side chain of alanine binds in a well-defined hydrophobic pocket characterized by conserved residues I263, L266, and K279 and partially conserved residue T277. Site-specific mutation of these residues leads to a significant loss in Ala-tRNA(Pro) hydrolysis, and altering the size of the pocket modulates the substrate specificity. Surprisingly, one ProRS INS domain variant displayed a complete switch in substrate specificity from alanine to cysteine.
Thursday, December 1, 2011
Chapter 11 Helpful Hints!
This video helps to conceptualize what is happening to the leading and lagging strands during transcription. The video starts out with a still picture that shows all of the relevant proteins. It then goes into an animation and shows how the leading strand is continuously synthesized, while the lagging strand is synthesized in pieces. It also shows how the lagging strand folds over so the DNA Polymerase can add nucleotides to the template strand.
This video is pretty cool! It is sooo fetch! It shows some of the processes that DNA goes through like coiling, replication, transcription and translation. It uses computer animation based on molecular research to show a 3-D view of what is happening during these amazing processes that DNA undergoes. Not only does it show the processes, but it also gives explanations about what is happening.
This video is pretty cool! It is sooo fetch! It shows some of the processes that DNA goes through like coiling, replication, transcription and translation. It uses computer animation based on molecular research to show a 3-D view of what is happening during these amazing processes that DNA undergoes. Not only does it show the processes, but it also gives explanations about what is happening.
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