Sunday, April 12, 2009
Inserted Genes
On page 99, Carroll mentions that process of finding species' relationships by the "study of...certain landmarks in specific places in species DNA", which are the result of "accidental insertions of junk DNA sequences near genes". Discuss the types of genetic point mutations, their relation to landmark DNA sequences, and their contribution to the evolution of different species.
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Point mutations occur every day in every organism. A point mutation can be called single base substitution, and it is a type of mutation that causes the replacement of single base nucleotide with another nucleotide of the genetic material. There is transition, a replacement of one nucleotide with another. There is transversion, where a pyrimidine replaces purine or vice versa. Another way to categorize point mutation is by its function. There are three categories: Nonsense mutations, missense mutations, and silent mutations. Nonsense mutations results in a premature stop codon, missense mutations result in code for a different amino acid and Silent mutations code for the same or different amino acid but there is no functional change in the protein.
ReplyDeleteNow we know what point mutations are, but we need to find out what land mark DNA sequences are in order to explain the relationship between those two. As Sean Carroll states in page 99 landmark DNA sequences are entered by point mutations and they are great way to trace genealogy of certain organisms. Recently, scientists have found a way to detect cancer DNAs with land mark genomic scanning. Shinji Hirostune, and izuho Hatada demonstrated that restriction landmark genomic scanning allowed them to screen 200-3000 restriction landmarks distributed on the genome simulataneously, and even low0 grade amplicfication could be detected effectively. Since the detection of the genomic DNA alteration in cancer tissues is an important step to clarify the mechanism of oncogenesis, they have found an effective way of learning cancer genes.
As we can see, different point mutations bring different landmark DNA sequences. This is how we detect our ancestors: by looking at specific landmarks in our DNA sequences. Even though point mutations do not create serious change in our genetic code, it gives slight change in our genes to trace any organisms’ genealogy. Point mutations help us to fine tune to our environment and sometimes, if it is favored by natural selection, those mutations can be passed on to next generation. Then, we can find landmark gene sequences to trace our steps back.
http://cancerres.aacrjournals.org/cgi/reprint/52/13/3642
http://en.wikipedia.org/wiki/Point_mutation
Genetic point mutations, often caused by chemicals or malfunction of DNA replication, exchange a single nucleotide for another. Most common is the transition that exchanges a purine for a purine or a pyrimidine for a pyrimidine. A transition can be caused by nitrous acid, base mis-pairing, or mutagenic base analogs. A point mutationscan be reversed by another point mutations, in which the nucleotide is changed back to its original state (true reversion) or by second-site reversion (a complementary mutations elsewhere that results in regained gene functionality). These changes are classified as transitions or transversions.
ReplyDeleteIn DNA there are certain landmarks that are produced by accidental insertion of junk DNA sequence near genes. There are long interspersed elements ( LINES) and short interspersed elements (SINES). When SINE and LINE is inserted there is no active mechanism for removing it. As Carroll points out “the insertion of these elements marks a gene in a species, and is then inherited by all species descended form it” (99). This connects to evolution. Once one mutation occurs in the DNA of on specie, it will later pass on the mutation to its off springs. Since this insertion of the element is very rare, when one two species share the same insertion is the same place the only explanation for it is that they share a common ancestor.
http://en.wikipedia.org/wiki/Point_mutation
http://www.genetichealth.com/g101_changes_in_dna.shtml
Landmarks in genes are used to trace back certain species to having similar ancestors. These “landmarks” discussed on page 99 are an insertion of “junk” DNA that is placed closely to a gene and therefore is less likely to have mutations and cannot be removed.
ReplyDeleteThere are many ways that this insertion of DNA can occur. Insertions are a category of mutation, but all mutations are not insertions. For an insertion of DNA there may be a frame shift mutation. In the frame shift mutation a sequence of DNA is added or deleted from the DNA and in affect causes a shift to occur in the entire thread of DNA. If groups of three are not inserted or removed, but rather just 1 or 2 DNA, there may be cause for new groups of 3 bases to be created causing there to be change in almost the entire DNA thread. Frame shift mutations normally occur through error in replicating the DNA. This may occur through an accidental recopying of a gene, causing repetition. It is also caused by transposable elements. These transposons are sequences of DNA that are able to jump around the genome and can be identified as class I or class II. Class I transposons can be transcribed to RNA and then back to DNA using reverse transcriptase. After this they are reinserted into another portion of the genome. For class II the gene is removed and placed into another location in the genome with the use of the enzyme, transposase. Frame shift mutation is normally what occurs in the addition of junk DNA near the gene.
For landmark DNA there are two different categories in which they are able to go under, SINES and LINES. SINES are short interspersed elements while LINES are long interspersed elements. These sequences of DNA, once inserted near genes, can be identified in a genome. Normally they are unaffected and so are passed on through descendents. If two species have the same LINE or SINE it is evidence that they had a similar ancestor. This is because the probability that these LINES or SINES occurring a the same place in a genome is so slim that it is almost guaranteed that if the same in two different species they had originated from the same ancestor.
There is a difference in point mutations and insertions. While insertions are adding or subtracting a new sequence of DNA codes, a point mutation is the replacement of a base for another. There are different types of point mutations that are able to occur in the genome; missense, nonsense, and silent. In a missense mutation the point mutation, or substitution of one DNA base to another causes the codon to code for an entirely different amino acid. This can cause diseases such as sickle cell disease in humans. For nonsense mutation the substitution of the DNA base causes the codon to become a stop codon. This causes the reading of the DNA to end prematurely causing certain codons to not be read and therefore their amino acids are uuencoded for. The final mutation may be a silent mutation. In this mutation, the point mutation makes no difference. This is because there are many different codons that can code for a single amino acid. The point mutation caused a code for an amino acid to change to a different code for the same amino acid. This means that the codon will still code for the same amino acid and there will be no change.
This is effective in the evolutionary process because with the use of natural selection these mutations allow a species to evolve. If a mutation occurs which ash an advantage for the survival of the organism, natural selection will occur and cause that mutation to spread throughout the species through reproduction. If the carrier of that mutation has a higher survival rate due to the slight advantage, it will have more chance of surviving and reproducing causing the trait from the mutation to spread due to natural selection. This connects with the landmarks because these sequences of genes that are more advantageous are more commonly used causing there to be a smaller chance for mutation. This is because the cell identifies this portion of gene to have significance in survival and so mutation is less likely to occur in that portion of the gene compared to a portion that is unused. If a sequence of DNA is found near a gene that is significant it can be kept unchanged and can be used as a landmark.
SINES and LINES are also important for evolution because they may cause mutations in a genome that can be beneficial to the organism. This will begin the process of natural selection and evolution as stated above.
SINES and LINES can be compared in species to find a connection in ancestors using gel electrophoresis and comparing similar bands that appear for the different species. By finding where certain splice sites are found can help in identifying ancestral pasts of species. An example of the evolutionary tree that can be created using this process is seen on page 101, and shows how the more sines or lines that a species have in common the more recent their same ancestor may have been.
http://en.wikipedia.org/wiki/Transposable_element
http://en.wikipedia.org/wiki/Mutation
http://en.wikipedia.org/wiki/Retrotransposon
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html
Recently, genes have been deciphered based on certain landmarks in the DNA whether than sequence similarity. Random insertions of DNA sequences have been added around the gene and are often recognized between two different species. One type of insertions are long interspersed elements (LINES). Another type are short interspersed elements (SINES). All species that descend from the species that acquired the insertion all inherit the insertion as well.
ReplyDeleteThis procedure is used for paternity testing in humans. The insertions that are added between the genes are so rare, that, if two species have the same insertion, that means that they are from direct lines of ancestry.
SINES and LINES are known as retrotransposons. They are both called non-LTR retrotransposons and SINES represent reverse-transcribed RNA molecules that were initially transcribed by RNA polymerase III into specific RNA like tRNA and rRNA. However, these sequences do not code for a functional reverse transcriptase protein.
SINES and LINES have been used to further research certain diseases. For example, HIV-1 is a retrovirus that acts like a retrotransposon. It contains both reverse transcriptase and integrase.
At least 34% of the human genome is made up of SINES or LINES. However, they have been often set aside as useless junk. Recently, there has been proof that SINES are actually beneficial at times and can relieve cells of physiological stress. Studies in the past have only researched the coding of proteins in DNA. SINES, therefore, were deemed as DNA without a function because they didn’t code for a specific protein or major nuclear RNA. However, there has been some evidence that SINES could code for a low-level transcript with some functional role or transcription in some other tissue.
Other hypotheses say that SINES could be a binding site for a chromosomal protein since they surround genes that have been deemed functional. They may also serve as a signal for chromosomal folding. Another hypothesis says that it is possible that these sequences of DNA have no function and may be present in the DNA for purely parasitic reasons.
http://genomicron.blogspot.com/2008/02/quotes-of-interest-sines-and-lines.html
http://en.wikipedia.org/wiki/Retrotransposon
http://www.ncbi.nlm.nih.gov/pubmed/12067657