Genetics Final.docx

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Biological Sciences
Rahul Warrior

Bio Final Review ADL8 Genomics: deals with DNASequence, organization, function and evolution of genomes - Made possible by Recombinant DNA o Gene Cloning and Genetic Engineering Metagenomics: genetic data derived from a community of organisms, usually microbial Bioinformatics: annotation of genomic sequences using computers Whole Genome Sequencing: starts with cloning and sequencing of short and random DNA fragments. This is not good for repetitive sequences Map-based (clone by clone sequencing): uses a physical map to assemble the fragments before sequencing them Contigs are continuous sequences of DNA assembled by smaller DNA fragments that overlap. De Novo Prediction: mutating a gene and predicting the location of the gene via the known mutation locus SNPVariation (Single Nucleotide Polymorphism): a mutation in a single base pair - This provides the largest number of human diversity Karyotyping: number of chromosomes in a eukaryotic cell Transcriptome: number of mRNAs in a cell at any given time - This changes as the cell reacts to the environment **RNAseq: can be used to determine the exons in a gene - mRNAis usually reverse transcripted to cDNA - this cDNAis then cut up; and placed against a reference genome to determine locations of exons on the DNA Comparative Genomics: is comparing genomes across species - Evolutionary signatures are genome comparisons between the past species and the current. - Phylogenetic Conservation suggests function; these regions are kept within evolutionary chains because the function is crucial to survival DNAMicroarray: chips that can contain up to 1,000,000 spots of DNAto measure the relative level of gene expression of genes. - These spots are usually florescent cDNA, and fluoresce relative to expression level - These cDNAbind to the Oligonucleotides on the chip o Oligonucleotides are single-stranded DNAthat help its complementary DNAbind to whatever the Oligonucleotide is bounded to Gene Expression Profiling: profiling multiple tissues at different time points to get an idea of what genes are doing HEXAGene: Mutations lead to Tay-Sachs Disease which is a hexosaminidaseAdeficiency and thus store up more gangliosides than normal. ADL9 Transgenic Organism: organism with genes from another organism - Introduced genes are called transgene o Need regulatory sequences to function Expression Vectors are vectors have the sequences needed for proper expression of transgenes - In bacteria there need to be promoters upstream the Cloning site, and a Shine-Dalgrano sequences in the 5’UTR for bacterial expression - Transgene must contain no introns o Multi-Cloning site: location with many restriction sequences for insertion of transgene, making recombinant DNA There may be Codon Bias, where an organism may not have some tRNAs Transgenic Plants: usually use Ti Plasmid from Soil Bacterium Agrobacterium - This bacteria has a tumor producing gene that can be knocked out and replaced with a functional gene - There is a disarmed vector with the transfer gene - There is a vector with the transformation gene which integrates the MCS into the plant genome o Round up ready plants are plants resistant to round up o Other plants have Bt gene inserted that kill pests when they eat plant Totipotent: a plant can be regenerated from a single isolated plant cell Animal Transformation: this alters the all the offspring of that animal - Animals are not totipotent and thus the transgenes must be injected into cells that give rise to gametes - Or can be injected into an embryo, and develop into a Genetic Chimera Forward Genetics: use a mutant phenotype to recognize a mutant gene then to identify the wild- type or mutant allele Reverse genetics: wild-type genes are cloned, mutated, and introduced back into the organism to study the phenotypic effects of mutation Pelements can also be placed into vectors, and a second vector with transposase will move the Pelement from the vector to the DNAof drosophila - We don’t want the Pelement and transposase to be on the same vector because later the Pelement may transpose out inside the host genome - This is gene will then be swapped out with the gene on the DNA - Using this homologous recombination method are position effects where most of the genome in eukeroytes are heterochromatic, and are poorly transcribed To test if homologous recombination as effective we use Positive-Negative selection where a negative genetic marker is put outside the region of homology and - The recombinant DNAis introduced into Embryonic Stem cells and implanted ina surrogate female and will develop into a chimera - This helps detect integration of the recombinant DNAin the wrong region of the chromosome (illegitimate recombination) - Introduction of transgenes may also lead to multiple insertions of that gene Reporter Genes are used to investigate gene regulation - Genes that usually express imaging capabilities when expressed and help illustrate how much a gene is being expressed Ectopicalally expressed genes are genes expressed in tissues not normally expressed Transcriptional Fusion: reporter genes tag regulatory sequences;
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