campbell 21 genomes + their evolution Flashcards

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approach for studying whole sets of genes and their interactions, from SEQUENCING of GENOME of any species

application of computational methods to store and analyze biological data, organizing the data from genomics

project for sequencing the entire human genome, publicly finded, 20 large sequencing centers in 6 countries + smaller labs for smaller projects

reference genome

a full sequence that best represents the genome of a species

determine complete nucleotide seq of each chromosome

sequencing machines, dideoxy (ddNTP) chain termination

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

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

national center for biotech info; maintained by nlm (lib of medicine) + nih (institute of health) Databases, software…

ncbi sequences database

software available on ncbi (basic local alignment search tool); compare a dna sequence w every sequence in genbank

common stretches of amino acids ## identifying protein coding genes and understanding their functions Goal: dna seq → id protein coding gene → id function

uses 3 lines of evidence to identify a gene Search for patterns that indicate gene presence

transcriptional, translational stop + start signals, rna splicing sites, telltale signs of protein coding genes (promotor sequences), short seq (specify mRNA)

expressed sequence tags::short seq (specify mRNA)

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

epigenetic features of the genome of hundreds of human cell types + tissue ### systems bio

approach of studying sets of proteins and their properties (abundance, modifications, interactions)

entire set of proteins expressed by a cell or group of cells

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

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

former games that have accumulated mutations over a long time and no longer produces functional protein , unique noncoding dna

repetitive DNA

consists of sequences present in multiple copies in the genome ## transposable elements and related sequences

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

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

protein that allows for the transposon dna property, encoded by transposon

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

shorter than most transposable elements, dont code for proteins but are transcribed into rna, some of which are thought to help in gene expression

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)

mistakes during dna replication/recombination Eg: duplications of long stretches of dna, simple sequence dna

stretcges if dba containing many copies of tandemly repeated short seq (2-500 nucleotide patterns)

series when a simple sequence dna strand unit is 2-5 nucleotides

whole genome shotgun sequences b/c short repeats hinders accurate fragment reassembly in computers, leads to sequences being permanent drafts!! ## genes and multigene families

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

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

enzyme helping protect animals against bacterial infections by hydrolyzing bacterial cell walls

nonenzymatic protein playing a role in milk production in mammals

lysozyme, alpha-lactalbumin, lysozyme

introns; facilitating the duplication of shuffling exons ## rearrangements of parts of genes: exon duplication and shuffling

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

increased or decreased production in one or more proteins

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

code transcription factors

transcription factor coding gene involved in speech acquisition in humans

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

evolutionary developmental biology; comparison of developmental processes of different multicellular organisms

encodes transcription factors regulating gene expression, specifying identity of body segments, all include homeoboxes

specific dna sequence, ~180 nucleotide bases long, codes for 60 amino acid homeodomain in encoded proteins

60 amino acid domain in an encoded protein; part of the protein that binds to DNA when the protein functions as a transcription factor