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Lecture 4

BIOC15 Lecture 4 Friday September 13.doc

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University of Toronto Scarborough
Biological Sciences
Karen Williams

BIOC15 Lecture 4 Friday September 13, 2013  Genomes  Genetics: DNA □ Transposable elements in ways they can alter DNA and cause mutations □ SNPs □ Future direction of genomics □ Looking at the level of DNA □ How do mutations change the DNA? Protein product? □ Ex. base pair substitution can have a specific effect on a protein product  Alkaptonuria □ Frameshift mutation □ One may be an insertion mutation that then changes the amino acids produced there after; one in exon 6 of the HGO gene, which may cause a deficiency at HA  Insertion / Frameshift mutation: in HGO □ Insertion at 119 leucine has a G inserted □ If a G is inserted you have a different mRNA made and a different sequence of amino acids after lecine  Sequence of part of a normal gene vs. Sequence of mutated gene □ Insertion of a GC base pair  changes mRNA template, which then changes the amino acids produced thereafter  Insertion sequence, IS1 □ Sometimes the insertion sequence can be identified by the repeats on either side □ Insertion is bacteria; there is a transposase source which allows the mobility of these insertion elements □ Important for p element mutagenesis in Drosophila  Unequal crossing-over can occur between homologous chromosomes □ Can get mutations by pairing between homologous chromosomes □ When bacterial sequences are inserted into the DNA, they not only insert a piece of DNA, but they also cause unequal crossing over  you get duplications on one strand and a deletion on the other □ Use process of homologous combination this to create site specific deletions in Drosophila melanogaster….?  Transposable elements (TEs) move around the genome □ Naturally these things occur because of transposable elements □ What causes this jumping? If you insert a bit of DNA causes a different amino acid and affect the proteins being made □ Two mechanisms - Can make a copy of themselves, original remains - They can insert to a new site on the genome, with no copy being mad □ Extremely important, because you can get foreign bits of DNA inserted into genes  Insertional mutagenesis: □ Could disrupt the gene so much, proteins will lack function (null) □ Due to homologous recombination and deletion in one part (we can make a null in that way)  remove sufficient amount of the gene to disrupt the production of the protein product (now the proteins encoded by that gene completely lack a function) □ Could be leaky; the protein that is a result of the insertion of mutagenesis could have some residual function  Tyrosinase-negative Oculocutaneous Albinism (Tyr) □ Oculo – I, Cutaneous- skin, albinism – lack of color □ Lack of pigment of eyes and skin □ Albinism biochemical pathway  you can see how it happens □ Full length of gene is not shown (indicated by ends) ; distance of gene is given as a scale □ Exon 2 is expanded; the normal sequence is missing C (between 1011 and 1012) where there is an insertion in the mutant □ The insertion is the mutation; wrote with part missing in the normal because it is not there (IT IS NOT A DELETION!) □ At position 292 at the polypeptide sequence; different amino acids are produced □ The insertion changes amino acids produced after it and causes a disruption of the tyrosinase gene so it is no longer functional in the production of tyrosine  Inserted Elements □ Insertion sequence (IS) elements that are inserted into a gene may disrupt the function □ Transposons inserted into the promoter region of a gene, may activate gene expression - We know the repeats sequence on either end – can identify presence of insertion element - Into the insertion element you put a clone fragment of a promoter of a particular gene - Using p element mutagenesis, insert that into the fly - Can employ what is a normal transposable element mutagenesis; what occurs naturally what happens when putting a fragment of a particular promoter into the fly  McClintock, Barbara: Transposable elements in maize □ Whole idea of transposable elements – people thought of genes as tiny little beads on a string that stay in place □ She noticed that corn is often purple or yellow - Purple – kernels that have pigment (C) - Colorless – kernels without pigment (c) □ Mottled kernels?  Can cross yellow with a purple corn plant? Yellow Purple - cc X C_ Possibilities - cc X CC ↓ Cc Purple - cc X Cc ↓ ½ Cc ½ cc Purple or Yellow □ Do not get mottled □ You come into every experiment with the idea of the theory that is going on? □ Then you look at the outcome, and ask does it match the theory? □ If it doesn’t, the theory could be wrong  Purple kernels, colourless and mottled kernels □ Theory that there are elements that promote transposition □ Ac activates transposition and Ds can transpose into the C gene locus  disrupted the production of colored pigment (get colorless kernel) □ When Ac activated transposition of Ds out of the C gene; element inserted in the c gene moves and jumps out of the c gene □ In some cells early on in development you may get production of color in those places (progenitor cells that derive from the cell that it hoped out are purple) and cells that derived from cells where it did not hop out, remain yellow  Excision of inserted element: Reversion □ Reversion of the c (colorless) to color in certain spots □ Excision of that insertion is a reversion mutation you get the mottled phenotype □ After many years, people finally saw how it works □ The transposase source is now known and is found in a lot of other organisms □ Our interpretation and assumptions going into the experiment may be wrong but examining our assumptions against what we see (our data), then how could we explain this data?  Science progresses Wild Type, Frameshift mutation by deletion, Reversion of deletion mutation by addition □ Reversions in Ames test □ Reverstion mutation that restores gene function- restores activity of the protein  How do transposable elements move between genome locations? □ They have a transposase source  Rice (Oryza sativa) □ We can find many transposable elements  How can mutants be detected? □ Conditional mutants – can get ones that are activated by heat or not □ Resistance mutations □ Use of all of these things and make bac
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