Biologia Genأ´mica 2آ؛ Semestre, 2017 Prof. Marcos Tأ؛lio ... Biologia Genأ´mica 2آ؛ Semestre, 2017

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  • Biologia Genômica

    2º Semestre, 2017

    Prof. Marcos Túlio Oliveira

    Departamento de Tecnologia

    Programa de Pós-Graduação em Biociências

    mtoliveria@fcav.unesp.br

    www.fcav.unesp.br/mtoliveria

    Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal

    Instituto de Biociências, Letras e Ciências Exatas de S.J.R.P.

    Universidade Estadual Paulista “Júlio de Mesquita Filho”

    mailto:mtoliveria@fcav.unesp.br http://www.fcav.unesp.br/mtoliveria

  • Biologia Genômica

    www.fcav.unesp.br/mtoliveira

    http://www.fcav.unesp.br/mtoliveira

  • Biologia Genômica

  • Biologia Genômica

  • http://virtuallaboratory.colorado.edu/Biofundamentals/lectureNotes-Revision/Topic4-2_GeneExp.htm

    Biologia Genômica

  • Apresentações dos alunos

    24/03

    Replicação do bacteriófago T4

    Replicação do bacteriófago ϕX174

    Replicação do plasmídeo ColE1

    Replicação do DNA cloroplastidial

    Replicação do vírus SV40

    Replicação do vírus HIV

    14/04

    Surgimento de genes “de novo”

    28/04

    O genoma do homen de Neandertal

    O genoma do homen de Denisova

    O genoma do chimpanzé

    05/05

    O genoma de Arabidopsis thaliana

    O genoma de Saccharomyces cerevisiae

    O genoma de Drosophila melanogaster

    O genoma do camundongo

    O genoma do boi

    O genoma da cana-de-açúcar

    O genoma de Xanthomonas

    Outros genomas...

  • www.fcav.unesp.br/mtoliveira

    Protein Science (2008), 17:385–388

    Biologia Genômica

    http://www.fcav.unesp.br/mtoliveira

  • http://www.sciencephoto.com/media/209697/view http://www.novusbio.com/Fas-Antibody_NBP1-89034.html

    Procariotos Eucariotos

  • Overview

    Molecular Biology of the Gene, 2003.

  • 6.1 Introduction FIGURE 01: The minimum gene number required for any type of organism

    increases with its complexity

    Photo of intracellular bacterium courtesy of Gregory P. Henderson and Grant J. Jensen, California Institute of Technology

    Photo of free-living bacterium courtesy of Karl O. Stetter, Universität Regensburg

    Photo of unicellular eukaryote courtesy of Eishi Noguchi, Drexel University College of Medicine

    Photo of multicellular eukaryote courtesy of Carolyn B. Marks and David H. Hall, Albert Einstein College of Medicine, Bronx, NY

    Lewin’s Genes X, 2009.

  • FIGURE 01: The minimum gene number required for any type of organism increases with its complexity

    6.1 Introduction

    Photo of higher plant courtesy of Keith Weller/USDA

    Photo of mammal © Photodisc

    Lewin’s Genes X, 2009.

  • 6.2 Prokaryotic Gene Numbers Range Over

    an Order of Magnitude

    • The minimum number of

    genes for a parasitic

    prokaryote is about 500;

    for a free-living

    nonparasitic prokaryote it

    is about 1500.

    FIGURE 02: Genome sizes and gene numbers are known from complete

    sequences for several organisms

    Lewin’s Genes X, 2009.

  • FIGURE 03: The number of genes in bacterial and archaeal genomes is proportional to genome size

    Lewin’s Genes X, 2009.

  • 6.3 Total Gene Number Is Known for

    Several Eukaryotes

    • There are 6000 genes in yeast; 18,500 in a worm; 13,600 in a fly; 25,000 in the small plant Arabidopsis; and probably 20,000 to 25,000 in mice and humans.

    FIGURE 04: The number of genes in a eukaryote varies

    from 6000 to 40,000 but does not

    correlate with the genome size or the complexity of the

    organism

    Lewin’s Genes X, 2009.

  • FIGURE 05: The S. cerevisiae genome of 13.5 Mb has 6000 genes, almost all uninterrupted

  • FIGURE 12: The average human gene is 27 kb long and has nine exons, usually comprising two longer exons at each end and seven internal exons

    Lewin’s Genes X, 2009.

  • Molecular Biology of the Gene, 2003.

  • 6.3 Total Gene Number Is Known for Several Eukaryotes

    FIGURE 06: Functions are known for only half the fly genes

    Adapted from Drosophila 12 Genomes Consortium, Nature 450 (2007): 203- 218.

    Lewin’s Genes X, 2009.

  • 6.4 How Many Different Types of Genes Are

    There?

    • The sum of the number of unique genes and the number

    of gene families is an estimate of the number of types of

    genes.

    FIGURE 07: Many genes are duplicated, and as a

    result the number of different gene families is much less than the total

    number of genes

    Lewin’s Genes X, 2009.

  • 6.4 How Many Different Types of Genes Are There?

    • orthologous genes

    (orthologs) – Related

    genes in different

    species.

    • The minimum size of

    the proteome can be

    estimated from the

    number of types of genes.

    FIGURE 09: The fly genome

    Lewin’s Genes X, 2009.

  • 6.5 The Human Genome Has Fewer Genes

    Than Originally Expected

    • Only 1% of the human genome consists of exons.

    • The exons comprise ~5% of each gene, so genes (exons plus introns) comprise ~25% of the genome.

    • The human genome has 20,000 to 25,000 genes.

    Lewin’s Genes X, 2009.

  • 6.7 The Y Chromosome Has Several

    Male-Specific Genes

    • The Y chromosome has ~60 genes that are expressed

    specifically in the testis.

    • The male-specific genes are present in multiple copies in

    repeated chromosomal segments.

    • Gene conversion between multiple copies allows the

    active genes to be maintained during evolution.

    FIGURE 15: The Y chromosome consists

    of X-transposed regions, X-

    degenerate regions, and amplicons

    Lewin’s Genes X, 2009.

  • 6.8 How Many Genes Are Essential?

    • Not all genes are essential. In yeast and flies, deletions of

  • 6.8 How Many Genes Are Essential?

    • We do not fully understand the persistence of genes that

    are apparently dispensable in the genome.

    FIGURE 17: A systematic analysis of loss of function for 86% of worm genes shows that only 10% have detectable effects on the phenotype

    Lewin’s Genes X, 2009.

  • 6.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell

    FIGURE 20: Hybridization between excess mRNA and cDNA

    FIGURE 21: The abundances of yeast mRNAs vary

    Lewin’s Genes X, 2009.

  • Estrutura

    Cromossomos, cromatina e nucleossomos

  • 9.3 The Bacterial Genome Is a Nucleoid

    • The bacterial nucleoid is ~80% DNA by mass and can be

    unfolded by agents that act on RNA or protein.

    • The proteins that are responsible for condensing the

    DNA have not been identified.

    Photo courtesy of the Molecular and Cell Biology Instructional Laboratory Program, University of California, Berkeley.

    FIGURE 05: A thin section shows the bacterial nucleoid as a compact mass in

    the center of the cell

    Lewin’s Genes X, 2009.

    Estrutura dos cromossomos

  • 9.4 The Bacterial Genome Is Supercoiled

    • The nucleoid has ~400

    independent negatively

    supercoiled domains.

    • The average density of

    supercoiling is ~1

    turn/100bp.

    FIGURE 07: The bacterial genome consists of a large number of

    loops of duplex DNA

    Lewin’s Genes X, 2009.

  • 9.5 Eukaryotic DNA Has Loops and

    Domains Attached to a Scaffold

    • DNA of interphase chromatin

    is negatively supercoiled into

    independent domains of ~85

    kb.

    • Metaphase chromosomes

    have a protein scaffold to

    which the loops of

    supercoiled DNA are

    attached.

    FIGURE 09: Histone-depleted chromosomes consist of a protein scaffold to which loops of

    DNA are anchored Reprinted from Cell, vol. 12, J. R. Paulson and U. K. Laemmli, The structure of histone-depleted

    metaphase chromosomes, pp. 817-828. Copyright 1977, with permission from Elsevier

    [http://www.sciencedirect.com/science/journal/00928674]. Photo courtesy of Ulrich K. Laemmli,

    University of Geneva, Switzerland.

    Lewin’s Genes X, 2009.

  • 9.7 Chromatin Is Divided into Euchromatin

    and Heterochromatin

    • Individual chromosomes can be seen only during mitosis.

    • During interphase, the general mass of chromatin is in the

    form of euchromatin, which is slightly less tightly packed

    than mitotic chromosomes.

    FIGURE 12: Regions of compact heterochromatin are clustered near the nucleolus and nuclear

    membrane

    Photo courtesy of Edmund Puvion, Centre National de la Recherche Scientifique Lewin’s Genes X, 2009.

  • Molecular Biology of the Gene, 2003.

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