front 1 # the human genome project fostered development of faster, less expensive sequencing techniques | back 1 no data |
front 2 genomics | back 2 approach for studying whole sets of genes and their interactions, from SEQUENCING of GENOME of any species |
front 3 bioinformatics | back 3 application of computational methods to store and analyze biological data, organizing the data from genomics |
front 4 human genome project | back 4 project for sequencing the entire human genome, publicly finded, 20 large sequencing centers in 6 countries + smaller labs for smaller projects |
front 5 in the human genome project, individuals’ dna was sequenced, scientists reviewed and agreed on a ___ | back 5 reference genome |
front 6 reference genome | back 6 a full sequence that best represents the genome of a species |
front 7 goal in mapping genome | back 7 determine complete nucleotide seq of each chromosome |
front 8 human genome mapping accomplished by | back 8 sequencing machines, dideoxy (ddNTP) chain termination |
front 9 whole genome shotgun approach | back 9 initial approach to map human genome; j craig venter 1.) cloning + seq random dna fragments (of randomly cut dna) 2.) computer assembles overlapping short seq into contin. Seq |
front 10 metagenomics | back 10 helped tech advances; (meta = beyond); dna from community of species collected from environmental sample then sequenced. Computer sorts partial seq + assembles into individual parts of species’ genome Advantage: can seq dna of mix microbial population, no need for culturing each species in lab # scientists use bioinformatics to analyze genomes and their functions ## centralized resources for analyzing genome sequences |
front 11 ncbi | back 11 national center for biotech info; maintained by nlm (lib of medicine) + nih (institute of health) Databases, software… |
front 12 genbank | back 12 ncbi sequences database |
front 13 blast | back 13 software available on ncbi (basic local alignment search tool); compare a dna sequence w every sequence in genbank |
front 14 Conserved domains | back 14 common stretches of amino acids ## identifying protein coding genes and understanding their functions Goal: dna seq → id protein coding gene → id function |
front 15 Gene annotation | back 15 uses 3 lines of evidence to identify a gene Search for patterns that indicate gene presence |
front 16 Gene presence indicator | back 16 transcriptional, translational stop + start signals, rna splicing sites, telltale signs of protein coding genes (promotor sequences), short seq (specify mRNA) |
front 17 ESTs | back 17 expressed sequence tags::short seq (specify mRNA) |
front 18 knocking out | back 18 blocking or disabling a gene to see how phenotype is affected. E.g. crispr cas9 system = technique used to block gene function ## understanding genes and gene expression at the systems level |
front 19 epigenome | back 19 epigenetic features of the genome of hundreds of human cell types + tissue ### systems bio |
front 20 proteomics | back 20 approach of studying sets of proteins and their properties (abundance, modifications, interactions) |
front 21 proteome | back 21 entire set of proteins expressed by a cell or group of cells |
front 22 systems biology | back 22 aims to model the dynamic behavior of both genes and proteins, the interactions among the system’s parts Gene and protein interaction networks in saccharomyces cerevisiae yeast, knock out pairs of genes to make doubly mutant cell. Fitness compared to single mutants, if matches, then genes didnt interact, if doesn't, then genes interacted ### application of systems bio + medicine |
front 23 metastatic tumors | back 23 tumors that have dispersed from primary tumors and invaded organs far away in the body # genomes vary in size, number of genes, gene density Difference in Mb (million base parts) between prokaryotes and eukaryotes, but not amongst eularyotes (jap canopy has 149000Mb, human 3000, no systematic relationship between genome and phenotype) ## number of genes How can humans (vertebrate) have nearly the same amount of genes as nematodes?::alternative splicing of rna transcripts, multiple proteins made from one gene in two ways: hundreds of alternatives and 2 alternatives only ## gene density and noncoding dna Humans have more base pairs than bacteria but less genes (more noncoding dna, alternative splicing), so density is lower than bacteria # multicellular eukaryotes have a lot of noncoding dna and many multigene families |
front 24 pseudogenes | back 24 former games that have accumulated mutations over a long time and no longer produces functional protein , unique noncoding dna |
front 25 most of DNA between functional genes are | back 25 repetitive DNA |
front 26 repetitive DNA | back 26 consists of sequences present in multiple copies in the genome ## transposable elements and related sequences |
front 27 transposable elements | back 27 stretch of dna in both pro and eukaruotes that can move from one location to another within the genome During transposition, these genetic elements move from one site in a cell’s dna to a diff target site by a recombination process Never detcach from dna, og and new dna sites js brought rlly close together by enzymes and other proteins (bending dna) Two types: transposon + retrotransposon ### transposon and retrotransposon movement |
front 28 transposons | back 28 transposable element; move within a genome by a dna intermediate Can cut and paste, removing original element from og site, Can copy and paste, leaving copy of og behind Both mechanisms require transposase, encoded by transposon |
front 29 Transposase | back 29 protein that allows for the transposon dna property, encoded by transposon |
front 30 retrotransposon | back 30 transposable element; move by means of an rna intermediate, a transcript of retrotransposon dna Always leaves a copy at the original site during transposition Synthesis of single strand rna intermediate of retrotransposon Reverse transcriptase synthesizes dna strand complementary to rna strand Reverse transcriptase synthesizes second dna, complementary to dna strand made in 2 Mobile copy of reverse transposon made and inserted (insertation) to new dna site ### sequences related to transposable elements |
front 31 alu elements | back 31 shorter than most transposable elements, dont code for proteins but are transcribed into rna, some of which are thought to help in gene expression |
front 32 line1/L1 | back 32 type of retrotransposon, longer than alu elements, low rate of transposition, transcription of these retrotransposons = crucial for development of early embryos Some transposable elements can encode proteins but these proteins dont carry out normal cellular function, so theyre still noncoding ## other repetitive dna (e.g. Single seq dna) |
front 33 repetitive dna not relatable to transposable elements probably arose from ___ | back 33 mistakes during dna replication/recombination Eg: duplications of long stretches of dna, simple sequence dna |
front 34 simple sequence dna | back 34 stretcges if dba containing many copies of tandemly repeated short seq (2-500 nucleotide patterns) |
front 35 short tandem repeat (STR) | back 35 series when a simple sequence dna strand unit is 2-5 nucleotides |
front 36 STRs provide challenges for | back 36 whole genome shotgun sequences b/c short repeats hinders accurate fragment reassembly in computers, leads to sequences being permanent drafts!! ## genes and multigene families |
front 37 multigene families | back 37 collections of two or more identical or very similar genes, arose from duplication from the same gene, like globin family # duplication, rearrangement, mutation of dna contribute to genome evolution ## duplication of entire chromosome sets |
front 38 what facilitates evolution of genes | back 38 polyploidy usually thru accident in meiosis (such as failure to separate homologs in meiosis 1). A set og polyploid genes can provide essential functions for an organism and it can accumulate mutations and diverge. Related to plant speciation ## alterations of chromosome structure ## duplication and divergence of gene size regions of dna |
front 39 lysozymes | back 39 enzyme helping protect animals against bacterial infections by hydrolyzing bacterial cell walls |
front 40 alpha-lactalbumin | back 40 nonenzymatic protein playing a role in milk production in mammals |
front 41 ___ present in birds but not rest of mammals. ___ is an evolved version of ___ (protein associated with key mammalian function of milk production | back 41 lysozyme, alpha-lactalbumin, lysozyme |
front 42 __ may have promoted evolution of new proteins by )) | back 42 introns; facilitating the duplication of shuffling exons ## rearrangements of parts of genes: exon duplication and shuffling |
front 43 exon shuffling | back 43 occasional mixing and matching of diff exons within a gene or two different genes (nonallelic). Could lead to new proteins with novel combinations of functions ## how transposable elements contribute to genome evolution |
front 44 if a transposable element inserts within a regulatory sequence, the transposition may lead to | back 44 increased or decreased production in one or more proteins |
front 45 transposable elements are thought to contribute to genome evolution in 3 ways | back 45 promote recombination, disrupt cellular genes/control elements, carry entire genes/individual exons to new locations # comparing genome sequences provides clues to evolution and development ## comparing genomes |
front 46 genes that differentiate humans from chimpanzees | back 46 code transcription factors |
front 47 FOXP2 | back 47 transcription factor coding gene involved in speech acquisition in humans |
front 48 copy number variants (cnv) | back 48 loci where some individuals have one or multiple copies of a particular gene or genetic region rather than the 2 standard copies (one on each homolog) Result from duplication or deletion inconsistent within the population Play a part in complex diseases and disorders; more likely to have phenotypic consequences bc on longer stretches of dna ## widespread conservation of developmental genes among animals |
front 49 evo-devo | back 49 evolutionary developmental biology; comparison of developmental processes of different multicellular organisms |
front 50 homeotic gene | back 50 encodes transcription factors regulating gene expression, specifying identity of body segments, all include homeoboxes |
front 51 homeobox | back 51 specific dna sequence, ~180 nucleotide bases long, codes for 60 amino acid homeodomain in encoded proteins |
front 52 homeodomain | back 52 60 amino acid domain in an encoded protein; part of the protein that binds to DNA when the protein functions as a transcription factor |