mapping in eukaryotes, mapping in phage, sex determination, chromosome mutations
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| subunit vaccines | consist of one or more surface proteins from the virus or bacteria
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| Hepatitis B viral vaccine | surface protein cloned into yeast expression vector, purified from yeast and packaged for use as a vaccine
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| Gardasil | recombinant capsid proteins provide immunity against HPV
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| edible vaccines | can be produced in food plants. decreas cost of production, avoids needles, no refrigeration required no need for sterile conditions to administer, constant source of recombinant protein
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| Bt transgenic crops | have built in insecticide protection to insect pests
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| gene testing is one of the first | successful applications of recombinant DNA technology
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| Two examples of prenatal tests | amniocentesis and chorionic villus sampling (CVS)
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| ASO's (allele-specific oligonucleotides) | short single stranded fragments of DNA; used as probes to identify different alleles; can differ by as little as one nucleotide (SNPs)
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| preimplantation genetic diagnosis (PGD) | genetic analysis of single cells from embryos created by in vitro fertilization
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| genotyping microarrays are used to | detect mutations in specific genes such as p53 which is commonly associated with cancers
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| genome scanning | allows analysis of DNA for dozens or hundreds of disease alleles
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| array comparative genomic hybridization (CGH) | a microarray technique, identifies copy number variations
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| genome wide association studies(GWAS) | identify genome variations that contribute to disease
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| gene therapy | transferring specific genes into mamalian cells to treat genetic disorders
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| severe combined immunodeficiency disease (SCID) | was the first disease to be treated with gene therapy
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| structural genomics | focuses on the sequencing of genomes, analyzing nucleotide sequences to identify genes/ gene regulatory elements
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| two methods to genome sequencing | 1)clone-by-clone method 2)whole genome shotgun method (shotgun cloning)
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| clone-by-clone method of genome sequencing | generates contigs that are aligned by restriction mapping; overlapping clones are sequenced. organized sequencing of contigs form a restriction map instead of random sequencing and assembly
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| shotgun cloning method of genomic sequencing | genomic DNA cut into contigs. overlapping sequenced fragments aligned using computer programs to assemble an entire chromosome; fragments aligned based on identical DNA sequences
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| bioinformatics | uses computer based approaches to organize, share and analyze data related to gene structure, gene sequence and expression, and protein structure and function
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| annotation | the process of identifying gene, their regulatory sequences and their functions
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| open reading frames (ORFs) | stretches of nucleotides that when translated to protein by computer analysis generate a series of amino acids prior to a stop codon; suggestive of a protein encoding gene
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| functional genomics | study of gene functions based on possible RNAs or proteins they encode;study of regulatory element function
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| orthologs | homologous genes in different species(arise through speciation)
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| paralogs | homologous genes in same species (arise through duplication)
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| single nucleotide polymorphisms (SNPs) | single base changes in the genome; many associated with disease conditions
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| copy number variations (CNVs) | segments of DNA that are duplicated or deleted
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| ENCODE (Encyclopedia of DNA Elements) | created with the aim to use both experimental approaches and bioinformatics to identify and analyze functional elements that regulate expression of human genes
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| Comparative Genomics | compares the genomes of different organisms in order to answer questions about genetics and other aspects of biology
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| eukaryotic genomes have several features not found in prokaryotes | 1)gene density that varies from chromosome to chromosome 2)introns 3)repetitive sequences
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| transcriptome analysis | studies gene expression qualitatively by identifying which genes are expressed and which are not; and quantitatively by measuring the varying levels of expression of different genes
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| microarray analysis | enables simultaneous analysis of all of a sample's expressed genes
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| proteomics | the identification and characterization and quantitative analysis of all proteins encoded by the genome of a cell, tissue, or organism
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| typical proteomic analysis | cells exposed to different conditions, proteins extracted, separated by 2DGE, spots of interest cut out, digested into peptide fragments and analyzed by mass spectrometry
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| systems biology | incorporates data from genomics, transcriptomics, proteomics,etc. to further elucidate components of interacting pathways
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| Pharmacogenomics | the study of how an individual's genetic makeup detemines the body's response to drugs
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| restriction enzymes | bind to a specific recognition sequence (restriction site); cleaves DNA to produce restriction fragments; most of these recognition sequences are palindromic; often cut in a staggered way, leaving "sticky ends"
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| plasmid | an extrachromosomal double-stranded DNA molecule that replicates independently from bacterial chromosomes
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| transformation | the process by which plasmids are introduced using calcium ions and brief heat shock to pulse DNA into cells; electroporation is an alternative to this method
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| cDNA libraries are prepared by | isolating mRNA from cells, synthesizing the complementary DNA using reverse transcriptase, and cloning the cDNA molecules into a vector
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| a restriction map of cloned DNA segment establishes | the number and order of restriction sites and the distance between restriction sites
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| southern blotting(DNA) is used to | find a particular clone in a library, characterize the size of the fragments from restriction digest, determine whether a clone conatains all or part of a gene
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| Northern blotting (RNA) is used to | determine whether a gene is actively being expressed in a given cell or tissue and to study the patterns of gene expressions in embryonic tissues, cancer and genetic disorders
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| Sanger sequencing | the most common method of DNA sequencing. also called dideoxynucleotide chain termination sequencing. it involves the addition of a small amount of one dideoxynucleotide(ddNTP)which causes DNA synthesis to terminate
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| Next generation sequencing | 1)DNA fragments on beads amplified by PCR 2)DNA on beads subjected to pyrosequencing reaction 3)light emitted by pyrosequencing reactions captured by detector
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| Stages of tumor development | 1)cell with genetic mutation 2)hyperplasia 3)dysplasia 4)in situ cancer 5)invasive cancer
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| clonal | orginated from a common ancestral cell that accumulated specific mutations
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| defects in cancer cells affect | genomic stability, DNA repair and chromatin modification
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| cancer cells have altered | DNA methylation patterns
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| histone modifications are ______ in cancer cells | disrupted
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| apoptosis | programmed cell death involving DNA fragmentation, digestion of cellular components, membrane blebbing, and apoptotic bodies being engulfed by phagocytes
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| the relative concentrations of the ____ and ___ proteins regulate apoptosis | Bcl2; BAX
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| regulation of levels of Bcl2 and BAX can | trigger or prevent apoptosis
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| cancer cells that overexpress Bcl2 are | resistant to chemotherapy/radiation
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| p53 | induces the expression of BAX; encodes transcription factor; can arrest the cell cycle at several phases; mutated in more than 50% of cancer cells
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| proto-oncogenes | normally stimulate cell proliferation. encode transcription factors, signal transduction molecules that stimulate cell division and cell cycle regulators
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| tumor suppressor genes | normally inhibit cell proliferation
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| oncogene | mutant proto-oncogene (GOF mutation;dominant); stimulates UNREGULATED cell proliferation
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| signal transduction initiates | a program of gene expression that propels the cell out of G0 and back into the cell cycle. cancer cells often have defects in signal transduction pathways
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| ras genes | encode signal transduction molecules
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| how does a proto-oncogene become an oncogene? | point mutation(ras); chromosomal translocation(CML); amplification (HER2)
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| oncogenes have two types | cellular (c-oncs); viral (v-oncs)
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| retroviruses can cause cancer by | activating a cellular proto-oncogene; carrying an oncogene into a cell;
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| acute transforming retroviruses | infect and transform normal cells into cancer cells (none identified in humans yet)
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| aneuploidy | an organism gains or loses one or more chromosomes
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| euploidy | complete haploid sets of chromosomes are present
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| polyploidy | more than two sets of chromosomes are present
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| reciprocal translocation | involves exchange of segments between nonhomologous chromosomes
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| Robertsonian translocation | breaks at the extreme ends of the short arms of two nonhomologous acrocentric chromosomes
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| Klinefelter's syndrome | male genitalia; XXY
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| Tuner syndrome | single X chromosome; female genitalia
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| human with three X chromosomes | female differentiation; often perfectly normal; sometimes underdeveloped secondary sex characteristics, sterility and mental retardation may occur
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| human with sex genotype XYY | males that tend to be over 6 feet tall
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| SRY absent in human embryo | female differentiation; wolffian duct degenerates; mullerian duct becomes the uterus
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| SRY present in human embryo | male differentiation; mullerian duct degenerates; wolffian duct develops into vas deferens
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| pseudoautosomal regions (PARs) on Y chromosome | have homology with regions on X chromosome
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| SRY encodes | for testes-determining factor which is a transcription factor that acts as a master switch to trigger the formation of testes
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| primary sex ratio | reflects the proportion of males to females conceived in a population
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| secondary sex ratio | reflects the proportion of each sex that is born
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| dosage compensation | balances the dose of X chromosome gene expression in males and females
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| Barr bodies | the inactive X is highly condensed and can be observed in stained interphase cells
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| Lyon hypothesis | X-inactivation occurs randomly in somatic cells
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| mechanism of inactivation of X | X-inactivation center(Xic) is active on the inactive X. it contains the X-inactive specific transcript (XIST) gene. XIST RNA coats the inactive X chromosome
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| bilateral gynandromorph | organisms with one X chromosome lost during the first mitotice division, making them half male and half female in some species
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| if two viruses simultaneously infect a bacterial cell, could recombination between them occur? | yes
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| intergenic recombination | recombination between two loci;
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| Seymour Benzer | produced a genetic map of the rII locus of phage T4
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| intragenic recombination in phage | simultaneous infection of e.coli by two mutant phages produces recombinant WT phages. the frequency is proportional to the distance between the two mutations
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| deletion mapping | provides a rough localization of each mutation. a point mutation is localized in the area of a deletion if it fails to give rise to any WT recombinants in complementation assays
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| crossing over | the reciprocal exchange of chromatid segments between homologous chromosomes; involves the breaking and rejoining of two chromatids)
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| chiasma | place on homologous pair of chromosomes at which exchange is occurring; site of crossing over
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| map units (also known as centimorgans) | are defined as 1% recombination between two genes on a chromosome
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| interference (in relation to crossing over) | reduces the expected number of multiple crossovers when a crossover event in one region of the chromosome inhibits a second event nearby; if interference is positive, there are less double crossovers than expected; if interference is negative,there r more
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| somatic cell hybridization | involves the fusion of two cells in culture to form a heterokaryon; nuclei then fuse to form a synkaryon from which chromosomes are lost at random
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| heterokaryon | a single hybrid cell with two nuclei
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| ordered tetrad analysis | can be used to map the centromere; determines map distance between a gene and the centromeres
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| unordered tetrad analysis | can be used to determine whether two genes are linked on the same chromosome and if so, map the distance between them
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