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by: Clotilde Boehm


Clotilde Boehm

GPA 3.65


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Class Notes
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This 14 page Class Notes was uploaded by Clotilde Boehm on Sunday October 25, 2015. The Class Notes belongs to BIOL 304 at University of Nevada - Las Vegas taught by Staff in Fall. Since its upload, it has received 15 views. For similar materials see /class/228640/biol-304-university-of-nevada-las-vegas in Biological Sciences at University of Nevada - Las Vegas.

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Date Created: 10/25/15
CLASS 14 013007 GENOME ORGANIZATION II A Genome Sequences and Gene Numbers gcont 1 Model eukaryotic systems Lot is known Genome sequence can directly test theories about genes Most common model systems a Yeasts Two closely related species sequenced Have similar Have similar Average size of gene Major differences i baker s y astgenomesarecompact ii S I 5 of S cerevisiae genes 200 bp have 1 intron on average Obo lntergenic Gene space lntrons 500 bp 43 of S pombe genes have introns Average interrupted gene has 2 introns Cnpynghl Q 2005 Pearson Prentice Hall lnc b Nematode worms C elegans Have regions Genome has Only 42 c Fruit y D Melanogasler Fly genome larger than C elegans Funding grepknqwn gr only half the fly ggnbs Only half d Mustard plant A lhaliana Has genome size w Transcrlpllon Signal lransducuon Translation ell ad esmn Prmem struclure Transporlerschannals 2n Cell cycledeath n DNA manlpulauon Enzymes Cytoskaleton Has more genes Many plants have duplicated segments CnpyngnllDZEIDG Pearson p rrrrr c2 Hall me Only 35 of A lhaliana genes Human genome surprises a Organization of the genome Haploid genome Only l accounted 1 of the hvumarni39genome codes for protein Average size of pro coding gene Average size of mRNA Approx 25000 genes predicted Difference in small number of genes can have drastic consequences Cnpyngm e 2003 Peamnn Prsrmre Hall In Many human genes The number of unique sequences b Gene distribution Are large gt500 Kb desert regions 20 of human genome 50 of human genome Repetitive transposon DNA has 3 The Proteome concept a Classifying genes Many genes are present in more than 1 copy 2 Family of related genes i Arise by ii Accumulation Important to score the number of different types of genes 2 As eukaryotic genomes get larger 2 i Number of ii Accumulate more members 30000 25000 39 20000 15000 10000 5000 7 Bacteriu m Yeast Fly A Worm A Copynghi 2006 Pearson Prentice Hall Inc Plant Man Families Families Unique with 2 4 with gt4 genes members members H in uenzae 89 1 0 1 S cerevisiae 72 1 9 9 D melanogaster 72 14 1 4 C elegans 55 20 26 A thaliana 35 24 41 Dopynnhr 2005 Pearson PIEIIIIIK Hall Im b De ning the proteome The number of proteins Core proteome Proteins are distributed Mitochondria 10 of volume 12 of prote Nucleus 7 of volume oof proteins lt3 o of proteins Copyright 2006 Pearson Prentice Hall Inc Orthologs a protein that is common to more than one species i Ortholog vs homolog Most fly genes are specific to the genus 100 ii Ortholog can be I de ned When 2 8 Specmc to genus proteins are E 60 w 2 an n 40 Common to all i eukaryotes Additional In 20 multlcellular eu karyotes Copynght 2006 Pearson Premlce Hall Inc c De ning how proteins Once total number of proteins known i Stable structural ii Transient Should allow for the de nition of the 4 Evolution of complex species Comparing the human genome and proteome Increasing complexity genes for metabolism replication transcription translation Functions Nervous system Immune system necessary for life 5x Cell compartments genes for organelles cytoskeletal components Multicellularity Development Copyright 2006 Pearson Prentice Hall Inc In progression from yeast to vertebrates F1nd addltlon of groups 200 of genes Transmembrane 1500 r Most new genes are concerned With Extracellular 1000 Intracellular 500 39 239 u Veast m E Copyright 2006 Pearson Prentice Hall inc I cupyright 2006 Pearson Prentice Hall Inc Human proteome has many Has few New proteins created by Essential genes The maintenance of a gene through evolution implies Test of an essential gene Need a functional test to de ne essential genes In many organisms test gene function by systematically deleting I kW fwe gis n f ia sEe lT Gene Cell expression structurefunction Unknown 20 m E E 15 a U 6 n 1o 7 7 i 5 25 c g r r r c E 9 am 9 9 9 9 u H u Q n m 395 E g 2 9 B C 395 E N E i 8 a u 3 a E c 2 9 g E E e 3 I E o e 9 v E o g n g o o i gt 6 o 9 a I39D E 0 Lu Total genome a Essential genes Copyright 2006 Pearson Prentice Hall Inc l MPSJtMiOKmTggeneequotare ndir ese ll 70 Nonviable 16 Growth defects 1 6 o Postembryonic phenotypes Copyright 2006 Pearson Prentice Hall Inc a Why are so few genes essential Organism has alternative ways Many genes are May have separate Need simultaneous inactivation b How to test for redundancy Combine non lethal mutations If double mutant dies 2 Systematically analyzed 6 Expressed genes Not all genes What is expressed in one tissue not expressed in another Some genes are expressed at a Abundance i Abundant RNAs 2 ii Scarce or complex RNA 2 Transcriptome Several analyses reveal that Most genes are expressed in all cell types 2 b Measuring expressed genes en masse New technologies allow for i SAGE 0 uses unique 0 measures ii HDA high density oligonucleotide arrays 0 spot DNA isolate all convert mRNA hybridize cDNA to Can compare two RNA pools from two cell type use different colored tags 39 wee RPB1 Fold change SRB1O 4 2 2 4 4 2 2 4 Copyright 2006 Pearson Prentice Hall Inc Comparing RNA Q0111 mutant Comparing SRBJO mutant with wildtype with wildtype RNA pol II SRBlO B Clusters and Repeats 1 Introduction 25000 human genes Members can be clustered a Tandem duplications Created When Can arise through Duplicates can separate When i Translocation moves ii Transposon mediated transfer b Gene clusters Can range from 2 adjacent related genes Unequal crossing over Unequal crossingover creates a duplication and a deletion Normal crossingover Gene 1 Gene 2 Chromosome1 0 Crossover Chromosome 2 Reciprocal recombinant chromosomes MWVVMMWV Unequal crossingover Mis aired WMAVAVWVK VM pargmal Crossover chromosomes 7W 3 II 1 II Nonreciprocal WWV recombinam chromosomes Copyright 2006 Pearson Prentice Hall Inc 10 c Highly repetitive DNA Tandem duplication can Often associated With Can also get expansionretraction Mouse satellite DNA forms a distinct band Find multiple tandem 33 Sam duplications of 1701 1690 Optical absorbance Buoyant density Copyright 2005 Pearson Prentice Hall Inc 2 Gene duplications and evolution Once gene is duplicated other copy Copy free to evolve Organisms not likely to a Both genes become necessary b One copy may become silenced ll 3 Globin clusters Ancient gene family involved in essential function Can compare sequences among In primates have 2 gene clusters a Alpha cluster contains 4 functional b Beta cluster contains 5 functional Expressed genes from each Globin proteins produced With different 2 llaw 110 GA 8 vviIB 58 10 20 30 40 50 kb Func onal Pseudo ene I 9 gene Copyrighl 2006 Pearson Prenuoe Hart Inn 2 uairn rlom Embryonic lt8 weeks 282 272 1282 21 Fetal 3 9 months a2 yg mi Adult from birth a2 52 a2 32 W W 4 luewdolenea Q Functional 1 Pseudogene Active gene gene Copyright 2006 Pearson Prentice Hall Inc 12 P Not all tandem repeats diverge rRNA is a In prokaryotes and eukaryotes rRNA Transcribed as Two rRNAs are then Multiple In eukaryotes can have Sequences for rRNA molecules are identical Sequences for spacers Unequal crossovers can change U Satellite DNA Synonymous With Often most DNA is Tandem repeats can Highly polymorphic in the population 2 Often found in regions of constitutive heterochromatin Satellite DNA often found at centromeres Types of satellite DNA 8 a In arthropods ate e II b In mammals m Cryptic Main repeat 0 Within each large 0 Within each sub repeat COHSCHSUS SCqUCIlCCS D virilis has four related satellites Predominant Total Genome sequence length proportion ACAAACT 7 O TGTTTGA 11 x10 250 ATAAACT 5 TATTTGA 36 X 10 8 ACAAATT 6 TGTTTAA 36 X 10 8 AATATAG TTATATC Cnpyllghl 20m Peamn Plenum Hall lnc 14


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