Sunday, April 12, 2009
Redundancy
On page 74, Carroll says "There are sixty-four different triplet combinations of A,C,G, and T in DNA, but just twenty amino acids". Explain the process by which DNA becomes a protein, specifically the steps where codons code for certain amino acids. What are the advantages/disadvantages for having several different combinations of codons code for the same amino acid? How can this redundancy lead to an advantageous, naturally-selected trait?
Subscribe to:
Post Comments (Atom)
The coding of a gene into a protein begins with the process of transcription, which is the synthesis of mRNA from the nucleotide bases of DNA, and ends with translation, the synthesis of the polypeptide. First is transcription. The promoter region of a gene contains a segment of nucleotides called the TATA box that is upstream from the targeted gene. Once a transcription factor binds to the promoter region of the gene, the DNA strands can begin to loosen. The transcription factor mediates the binding of RNA polymerase II to the DNA as more transcription factors are added to eventually form the transcription initiation complex. The RNA polymerase II begins to divide the DNA helix structure into separate strands and add nucleotides at the 3 prime end, adding base complementary RNA base pairs. The double helix reforms behind the RNA polymerase II. Another additional feature is the simultaneous transcription of the targeted gene with several RNA polymerase II molecules, synthesizing many copies of mRNA for bulk protein translation. As the mRNA elongates, a termination sequence of AAUAAA signals the end of the mRNA, but it continues for several more nucleotides and ends where a polyA tail will be added.
ReplyDeleteBefore the mRNA is translated in the cytoplasm, it undergoes RNA processing. First the 5 prime end is fitted with a modified guanosine triphosphate and the 3 prime end of the pre-RNA is fitted with a polyA tail. The guanosine cap is protection against degradation and help in signaling attachment of ribosomes to the mRNA as does the polyA chain in addition to transporting the mRNA out of the nucleus. The pre-mRNA also undergoes RNA splicing which realizes the idea that the mRNA contains introns and exons that are noncoding and coding regions. These regions of noncoding and coding mRNA can alternate between the expression of different proteins for the same primary transcriptional mRNA unit, demonstrating the ability of genes to code for several different proteins. RNA spicing is carried out first by small nuclear ribonucleoproteins (snRNPs) that recognize the ends of introns and join with other proteins to create a spliceosome. The spliceosome carries out RNA splicing by cutting at specific sites to take out introns and join together regions of exons. Then the edited mRNA leaves the nucleus and enters the cytoplasm of the cell.
Transcription occurs after translation. The guanosine cap signals the attachment of a small ribosomal subunit to the mRNA, which is made of proteins and ribosomal RNA. Then the AUG initiation codon signals the start of translation. Translation revolves around the use of transfer RNA or tRNA. The structure of a tRNA is the combination of a bonded amino acid at the 3 prime end, which is facilitated by aminoacyl-tRNA synthetase, and an anticodon within the tRNA. The first example of redundancy is seen in these tRNA complexes with wobble. Wobble is the relaxation of pairing restrictions in tRNA so that the base U in the third position of the anticodon can pair with either an A or G and inosine (I) can pair with either U,C, or A. This relaxation of pairing bases does not affect the outcome of the needed amino acid in the polypeptide chain as the variable combinations all code for a single particular base. So with the initiation of translation with the codon AUG, tRNA carrying the amino acid methionine attaches to the AUG triplet base pair. After this process, a large ribosomal unit attaches to this structure to create the translation initiation complex and the combination of these components are facilitated by initiation factors. This places the initiation tRNA in the P Peptidyl-tRNA binding site of the ribosomal complex. Then with elongation factors the mRNA is read to code for a specific tRNA that enters in the A Aminoacyl-tRNA binding site. Then ribosome then catalyzes the formation of a peptide bond between the two adjacent amino acids. Then translocation occurs with initial tRNA in the E exit site of the ribosomal complex and the tRNA containing the elongation polypeptide chain relocating to the P site. Then the mRNA is read further for another tRNA and another amino acid to add to the polypeptide chain entering the A site of the ribosomal complex. Eventually a stop codon of either UAG,UAA, or UGA causes the incorporation of a release factor that frees the polypeptide chain from the last tRNA and the ribosomal complex disassembles.
As the ribosomal unit synthesizes the new polypeptide chain, it begins to fold and coil itself with specific hydrogen bonding to create a structural protein with complicated structure. Other posttranscriptional modifications add additions to particular amino acids but this completes the process of a gene coding a protein.
The redundancy of the genetic code is found with the fact that only two amino acids are coded by one codon (methionine and tryptophan) while the rest are coded by several codons. Most amino acids that are coded by several codons differ specifically in the third position of the triplet is related to the concept of wobble. The evolutionary benefit of having several different codons code for the same amino acid is the protection against mutations that could significantly change the conformation of the protein and its function. Especially against base-pair substitutions, due to the wobble of tRNA and the fact that several codons code for the same amino acid, the production of proteins can be protection from a differentiating structure. The idea of silent mutations comes from this leeway and relaxation of codon and amino acid pairing. There is a less probable chance that there will be a change in protein structure. There could have been evolutionary pressure toward the retention of protein structural information in the genetic code. While mutations can be harmful, through the miss construction of proteins that rely on its specific structure, the disadvantage of protection against mutations in having several different combination of codons code for the same amino acid is the rarity of mutations. Mutations serve as the primary sources of variability and alternative combinations of traits that could benefit survival of a particular species so with this preventative measure, the occasion that mutation occurs for a trait is rare. There is less variability in the selective gene pool of species’ populations.
This redundancy can lead to an advantageous naturally-selected trait by only retaining mutations in the genetic code that is advantageous for that particular species’ populations survival. While disadvantageous mutations that pass the redundancy of codon pairing are eliminated from the selective gene pool through the lessened survival of the organism containing that particular variation, an advantageous mutation that surpasses the test of redundancy and be continued through the survival of that variation.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
http://en.wikipedia.org/wiki/Messenger_RNA
http://books.google.com/books?id=h59BWkO5c1oC&pg=PA156&lpg=PA156&dq=codon+amino+acid+redundancy&source=bl&ots=p0JycDuTgu&sig=vAOV7hFXyJ1_56O_kReQqhjb9Z8&hl=en&ei=5vTiScrbI9bgnQeSwuihCQ&sa=X&oi=book_result&ct=result&resnum=2#PPA157,M1
The redundancy of the genetic code allows different triplets of bases to encode the same amino acid. These synonymous changes show the conservative face of natural selection, “running in place”, and allows for immortal genes. When the genes of humans and tomatoes are compared, 83 % of the genes positions are identical, while 96% of the encoded proteins are identical. The insignificant mutations were allowed to accumulate, since they do not alter the encoded proteins crucial for survival. This redundancy reduces the chance of vital proteins becoming mutated and decreasing the survival rate of the organisms, by having multiple codons translate into the same amino acid. For example, the amino acid leucine is encoded by six different codons. Since most amino acids are encoded by at least two different triplets, triplets in DNA sequences can “run” (change from sequence to sequence) but selection usually sees to it that they do not run so far as to change the protein’s sequence and function (Carroll 82).
ReplyDeleteAnother advantage of redundancy in genes encoding for the same amino acid is the possibility of different means to similar ends. The four different venom from the black mamaba, sea anemone, a scorpion, and a marine cone shell snail all are encoded by different DNA sequences. Carroll states that “given sufficient time, identical or equivalent mutations will arise repeatedly by chance, and their fate (preservation or elimination) will be determined by the conditions of selection upon the traits they affect (Carroll 155).” The advantage of multiple codons encoding the same amino acid can be seen in the violet-sensing and UV-sensing birds. The violet-sensing and UV-sensing capabilities correlate with a particular amino acid at position 90 in the SWS opsin. Birds with a serine amino acid are tuned to violet, while birds with a cysteine are tuned to UV. The single mutation at position 268 from A to T will occur in roughly 750 million offsprings. Owever, given the number of offsprings every year and time, a serine-to-cystein switch will arise once every 750 years. When regarding the long evolutionary time, it is likely that random mutations occur multiple times and repeat itself to be selective advantages. The fact that multiple codons code for the same amino acid increases the chance of random mutations encoding for the same amino acid in different species, providing the evolutionary change of different species with similar functions. These random mutations that occur throughout evolutionary time can happen in many different species, and these 4 different phyla that have venom that block potassium channels were proved to be advantageous in their survival, so natural selection preserved the gene and prevented it from becoming fossilized. The redundancy of the genetic sequences increases the chance of random mutations in different species that provide the same selective advantage and preservation due to natural selection.
http://en.wikipedia.org/wiki/Cone_snail#Harpoon_and_venoms
http://www.krugerpark.co.za/africa_black_mamba.html
There is an intricate process that allows for the production of amino acids through the codons on DNA. To create an amino acid mRNA is required and is linked with a particular amino acid.
ReplyDeleteTo begin the process the enzyme RNA polymerase separated the DNA strands and adds on RNA bases. The RNA polymerase begins and knows where to attach on a DNA strand because of the promoter, which is a sequence that signals the RNA polymerase to attach and begin transcription. A crucial promoter sequence of the DNA sequence is the TATA box. Next RNA polymerase moves along DNA 10-20 bases at a time. While the DNA winds back the new RNA molecules peel away to create mRNA. In the process of transcription many RNA polymerase molecules can follow one after another to copy the same gene multiple times. Finally there is the terminator that signals the enzyme RNA polymerase to stop transcription. For eukaryotic cells the polymerase will actually continue past the signal (AAUAAA) while in prokaryotes the transcription will stop right at the termination signal.
After the mRNA has gone through transcription it will be modified and edited. The 3’ cap will have a poly (A) tail that consists of 50-250 a nucleotides. This will inhibit the degradation of the mRNA and help ribosomes attach and facilitate the export of mRNA from nucleus. There is also the enzyme, spliceosome, which cuts between exons and introns. These are different segments of the RNA that are both used in coding for proteins and are not used. The introns are cut away and the exons are then attached by the spliceosome and used.
Translation then occurs, which is the synthesis of the protein. The tRNA, which are lengths of RNA that are transcribed from DNA templates. Each of these tRNA are paired with an amino acid. Due to the wobble affect more than one tRNA can match up with the same amino acid. There are three stages to translation; initiation, elongation and termination. In translation codons, three bases, are used in reading for the amino acid code. In initiation the ribosomal unit attaches to the strand of mRNA on the 5’ end and moves downstream till it hits AUG, the start codon. Then a large ribosomal subunit attaches along with the tRNA at the start codon and begins the next stage of elongation. In elongation there is codon recognition where hydrogen bonds are formed at the A site with mRNA and tRNA. Next the peptide bonds are formed by the rRNA molecule of the large ribosomal subunit that catalyzes the formation of peptide bonds and joins amino acids in the A site. Then translocation occurs where the tRNA moves to a new site with the mRNA. The ribosomal unit continues to move downstream till termination occurs with the stop codon that causes the ribosome to release the polypeptide. This is how a protein is made.
This process is very effective because of the use of introns and exons and also the wobble effect. Since there are many different codons that can code for a single amino acid there are different combination of DNA codes that can create the same protein. This is helpful with the use of the introns and exons. Since splice sites are different, there may be multiple proteins that can be coded from the same site of DNA. This is because different portions of that same mRNA that is copied from the same portion of DNA can be introns or exons depending on the splice site. Because of this, the same portion of DNA can be coded for production of multiple different proteins.
There are many advantages in having the wobble affect in protein synthesis. Because mutations can occur on a gene segment, the wobble affect decreases the probability that a mutation will impact the outcome of the gene. If there are many different codons for the same amino acid, a point mutation may just cause a slightly altered codon that codes for the same amino acid. This would cause there to be no change in the protein synthesis. This can be seen on pages 82-83 where the idea of natural selection on this wobble affect is discussed. If a mutation is not fatal to the organism natural selection will allow the mutation to be persistent because there is no harm. This also allows natural selection to “’rigidly destroy injurious variations.’”
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
http://bbwiki.tamu.edu/index.php?title=Wobble_effect
http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.php