Lecture 3 Midterm Exam Notes.docx

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University of Toronto Scarborough
Biological Sciences
Dan Riggs

BIOB11- Lecture 3- Genome Evolution and Introduction to the Central Dogma of Molecular Genetics Vocabulary: Transposition: movement of DNA segments that move from one place on a chromosome to a completely different site, often expressing gene expression. Transposon: DNA segments capable of moving from one place in the genome to another. Retrotransposon: Transposable elements that require reverse transcriptase for their movements within the genome. Reverse Transcriptase: An RNA-dependent DNA polymerase. An enzyme that uses RNA as a template to synthesize a complementary strand of DNA. (An enzyme that is found in RNA- containing viruses and used in the laboratory to synthesize cDNA. Centimorgan: a map unit of recombination; 1cM=1% recombination between two linked genes. Genetic Map: Assignment of genetic markers to relative positions on a chromosome based on crossover frequency. Physical Map: Polymorphism: Sites along the DNA where differences exist in a population RFLP -restriction fragment length polymorphism: a base change resulting in abolition or creation of a recognition sequence for a restriction enzyme. Single Nucleotide Polymorphisms (SNP): Sites in the genome where alternate bases are found with high frequency in the population. SNP‟s are excellent genetic markers for genome mapping studies. Lecture 3 Notes: Gene mapping, Figure 10-30 Things that can happen - during unequal crossing over. Fuzzy chromosome imageSame chromosome but one has suffered an inversion Some cancers are due to inversions etc. on a chromosome -IMPORTANT FIGURE!!! Mobile genetic elements: Transposons Transposition •Transposon/transposable element -transposition means change of position from one place to another. Barbara McClintock: „controlling elements of maize (corn)‟ Nobel prize in 1983 Experiment: gene C (corn) A transposable element is inserted into the color gene at make it a colorless kernels. Can this transposable element now jump out of the gene? If late then some purple some clear (spot) If it is out early in development then mostly purple -Larger sectors due to transposon jump early in development Transposable elements do not have a goal site, they can jump into a random site (called recipient or target site) -no need to memorize random (AATTC) sequence. -the transposon inserts into the recipient DNA -the ends of the transposon are comprised of inverted repeats (in red) Inverted repeat – the same sequence from 5‟ to 3‟ but arranged in a inverted order (flipped horizontally and vertically) Direct Repeat- the same sequence from 5‟ to 3‟ in the same direction and order The transposon has a protein that recognizes the inverted repeats so if it needs to jump somewhere else, the protein recognizes that it need to collect all the DNA between the two inverted repeats. The inverted repeats are flanked on either side by the direct repeats Generation of Direct Repeat 1. First find a sequence – target site 2. The enzyme transposase encoded by the transposon which acts on DNA and makes staggered cuts 3. the end structure has a partial single stranded structure hanging 4. The transposon then enters the gap and host enzymes come in and repair the DNA using the complementary base pairs of the end structures creating a direct repeat sequence. - this is like a “cut and paste method” In a bacteria, the primary method for a transposon moving is for transposase to catalyze its incision from one side and its insertion in the other side Transposase binds to the region of dna and recognizes the sequence and then two molecules of transposase hold on to the molecule and cut it (staggered cut) Then it inserts itself and repairs the ends This Cut and paste method is also known as non replicative transposition because there is no replication. Foot print of transposon is short repeats on both sides when the transposon was removed – shows some evolutionary proof of the insertion - possibility Replicative – called retrotransposons -first transcription occurs and transcribes the entire transposable element. -then reverse transcriptase (enzyme) converts a single stranded cDNA to a double stranded cDNA -then it goes to the recipient site and transposase catalyzes the new DNA -So now instead of having 1 copy of the transposon in a certain place, now we have two  it never left the donor DNA, just a copy of it went to a different site -A consequence of transposition is that anytime you are moving from one place to another or inserting to an important place, there is chance of mutation. A consequence of replicative transposition is that now there is double the amount of transposon that exists and this is what makes some genomes very large Half of the sequences of our genome is derived from once active transposable element that had spread themselves around the genome – most of them are now inactive Genetic and Molecular Mapping of Genes (at different levels) The “Genetics” approach: examine recombination frequency between two traits (usually visible) to estimate the distance between two linked genes. –Mendelian -use the two traits and how often they segregate together or apart to estimate the difference between two linked genes. “LINKED” - genes that are on the same chromosomes not different ones •Distance between genes on a chromosome is proportional to probability that recombination will occur between them. (see example) •Centimorgan: a map unit of recombination; 1cM=1% recombination between two linked genes. The red denotes one parent and the black denotes the other parent red and black are two non-sister chromatids (imagine that each black and red has a sister chromatid but we only look at the two that are participating in recombination) Here we imagine that any of the three crossovers will occur but actually, recombination is random so it could occur at the top, bottom, middle , etc -if the genes are far apart (like genes A and C at the ends of the chromosome) then any of those crossovers will separate the parental alleles from one another -then the microtubules connect and pull in opposite directions  so if crossing over occurred then it will pull part of the other chromatid along with it - if the two genes are close together (like A and B) of the three possible combinations only one will lead to recombinance of A and B - Thus, the % recombination between two genes is proportional to the distance between them The cross over happens at Aa site and then the microtubules come and separate the two strands and now one has A b c and the ot
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