aula 3 2023-24

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<p>Genes, genomas e cromossomas.</p><p>Organização geral dos genes de procariotas e eucariotas.</p><p>Genomas de plasmídeos, vírus, organelos, procariotas e eucariotas. O paradoxo</p><p>do valor C. DNA codificante e não codificante. Sequências repetitivas.</p><p>Empacotamento do DNA. Composição, organização e remodelação da cromatina.</p><p>Estrutura dos cromossomas e marcadores citogenéticos visíveis.</p><p>Genes, genomes and chromosomes.</p><p>General organization of prokaryotic and eukaryotic genes.</p><p>Genomes of plasmids, viruses, organelles, prokaryotes and eukaryotes. The</p><p>paradox of the value C. DNA encoding and non-coding. Repetitive sequences.</p><p>DNA packaging. Composition, organization and remodeling of chromatin.</p><p>Structure of chromosomes and visible cytogenetic markers.</p><p>1</p><p>GENÉTICA 2023-24 | GENETICS 2023-24</p><p>AULA 3 | LESSON 3</p><p>Are genes and genomes similar in all</p><p>organisms?</p><p>• Are all genes similar?</p><p>• Are all genomes organized in the same way in all organisms?</p><p>2</p><p>Genes</p><p>• DNA region capable of being transcribed into a functional or</p><p>informational RNA</p><p>• regions regulating the beginning of transcription capable of</p><p>responding to chemical signals from the environment or</p><p>other parts of the genome</p><p>• regulatory region at the end of the transcription</p><p>3</p><p>Prokaryotic genes</p><p>• regulatory proteins bind to the regulatory region of the gene and initiate</p><p>transcription of the adjacent coding region</p><p>• in prokaryotic genes the coding region is continuous</p><p>4</p><p>Prokaryotic genes</p><p>• some prokaryotic genes are organized in operons, controlled by common</p><p>regulatory regions</p><p>• polycistronic mRNAs</p><p>5</p><p>Eukaryotic genes</p><p>• eukaryotic genes contain introns</p><p>• introns are transcribed and later excised from the original transcript</p><p>• introns are part of the gene and are important to produce a certain</p><p>sequence and dimension transcript in the right space and time</p><p>6</p><p>Eukaryotic genes</p><p>7</p><p>Genome sizes</p><p>Genomes</p><p>Viroids and obelisks?</p><p>• https://zap.aeiou.pt/e-uma-loucura-nova-classe-de-vida-descoberta-</p><p>no-sistema-digestivo-humano-580489</p><p>10</p><p>Plasmid genomes</p><p>• extra-chromosomal DNA.</p><p>• most common in bacteria</p><p>• usually circular in bacterial cells</p><p>• non-essential genes</p><p>• replication equipment encoded in the</p><p>genome of the carrier cell.</p><p>Eukaryotic organelles</p><p>• mitochondria and chloroplasts have dsDNA</p><p>genomes</p><p>• multiple identical copies of its chromosomes</p><p>• mostly circular; some have introns</p><p>• genes directly related to the function; no</p><p>overlapping with nuclear gene</p><p>• endosymbiont theory of organelle origin</p><p>Viral genomes</p><p>I. dsDNA</p><p>II. ssDNA(+) with a dsDNA</p><p>intermediate</p><p>III. dsRNA</p><p>IV. (+)ssRNA with a (-)ssRNA</p><p>intermediate</p><p>V. (-)ssRNA</p><p>VI. ss(+)RNA-RT with</p><p>(-)DNA/(+)RNA intermediates</p><p>VII. ds gapped DNA</p><p>Baltimore classification</p><p>Prokaryote genome</p><p>• dsDNA</p><p>• typically, one chromosome</p><p>• packed in a nucleoid</p><p>• are introns are rare</p><p>• few intergenic regions</p><p>Eukaryote genomes</p><p>• nuclear chromosomes</p><p>– haploids, diploids and polyploids</p><p>– homologous chromosomes</p><p>Eukaryote genomes</p><p>DNA contains the genetic information:</p><p>the principle of colinearity between DNA and aminoacid sequences (Jacob and Monod)</p><p>17</p><p>Genome sizes</p><p>Relationship between genome size and complexity:</p><p>C-value paradox</p><p>19</p><p>The minimal genome concept</p><p>• the set of genes sufficient for life to exist and propagate under nutrient-rich and</p><p>stress-free conditions</p><p>20</p><p>Mycoplasma laboratorium (Synthia)</p><p>Non-coding DNA</p><p>21</p><p>The number of exons (number of introns +1) varies</p><p>between genes of different organisms</p><p>22</p><p>Repetitive DNA in eukaryotes</p><p>23</p><p>• different types of units appear in "tandem" or dispersed throughout the</p><p>genome</p><p>• many of the repeated sequences originate from moving genetic elements</p><p>Repetitive DNA</p><p>24</p><p>Repetitive DNA</p><p>25</p><p>26</p><p>Tandem repeats</p><p>Intespersed elements</p><p>27</p><p>• LINEs long interspersed elements</p><p>• SINEs short interspersed elements</p><p>• LTR long terminal repeats</p><p>Repetitive elements in a human gene</p><p>28</p><p>SINEs: Alu element</p><p>• 200 nucleotides</p><p>• restriction site</p><p>• 106 copies</p><p>• 10% of the human genome</p><p>https://www.youtube.com/watch?v=Cy9dTDbr</p><p>-dM</p><p>• DNA fingerprinting</p><p>https://www.youtube.com/watch?v=7onjVBsQwQ8</p><p>29</p><p>Genome packaging</p><p>Long DNA molecules are packed in a relatively small volume</p><p>30</p><p>Viral genome packaging</p><p>genetic material packed in the virus head is functionally inert</p><p>31</p><p>(a) l phage head (0.1 mm); (b) l phage chromosome (17 mm long)</p><p>Viral genome packaging</p><p>32</p><p>large dsDNA viruses encode a powerful DNA-translocating machinery that</p><p>encapsidates a viral genome into a preassembled capsid or procapsid</p><p></p><p>Bacterial genome packaging</p><p>33</p><p>Electron micrographs of isolated E. coli nucleoids after spreading the DNA on</p><p>protein monolayers. (Left) Membrane-free nucleoid (bar, 1 μm). (Right)</p><p>Membrane-associated nucleoid. Micrographs courtesy of R. Kavenoff.</p><p></p><p>Bacterial genome packaging</p><p>34</p><p>E. coli has a large circular chromosome (1,200 mm) packed in a 2 mm-length cell, by</p><p>association with histone-like nucleoid structuring proteins</p><p>Bacterial genome packaging</p><p>35By Subhash C. Verma, Zhong Qian, Sankar L. Adhya - doi:10.1371/journal.pgen.1008456 Verma SC, Qian Z, Adhya SL (2019) Architecture of</p><p>the Escherichia coli nucleoid. PLoS Genet 15(12): e1008456., CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=84998327</p><p>NAP - Nucleoid-associated proteins:</p><p>• Small and abundant</p><p>• Positively charged</p><p>• Regulate gene activity</p><p>Supercoiling of viral</p><p>and bacterial genomes</p><p>tightens the packaging</p><p>36</p><p>• Topoisomers: identical molecules</p><p>that differ only in their linking</p><p>number (L)</p><p>• Topoisomerases: cut one (Type I) or</p><p>both (Type II) strands and wind or</p><p>unwind the helix</p><p>Supercoiling of plasmid DNA:</p><p>the secret of the 3 bands</p><p>37</p><p>DNA packaging in nuclear chromosomes</p><p>tight packaging of large genomes in the nucleus involves DNA-protein interactions</p><p>each human chromosome ranges 19,000 to 73,000 μm in length</p><p>the human nucleus (5-10 μm diameter) contains 2 m of DNA</p><p>DNA packaging in nuclear chromosomes</p><p>39</p><p>chromatin has a substantial amount of protein:</p><p>• Non-histones: less positivelly charged</p><p>• Histones: positivelly charged</p><p>Nucleosomes</p><p>40</p><p>• digestion with endonucleases produces</p><p>fragments with approximately 200 bp in</p><p>length, or multiples thereof</p><p>• electron microscopy shows linear arrays</p><p>of spherical beads</p><p>• chemical analyses show 2 types of</p><p>tetramers</p><p>(H2A)2(H2B)2</p><p>(H3)2(H4)2</p><p>• extended digestion producers the</p><p>nucleosome core particle with 147 bp</p><p>• linker DNA associated with histone H1</p><p>41</p><p>Nucleosomes: the 11 nm fiber</p><p>42</p><p>Solenoid: the 30 nm fiber</p><p>Supercoiling: the 300 nm fiber</p><p>43</p><p>44</p><p>Metaphase chromosomes</p><p>the highest degree of condensation</p><p>Chromatin remodeling</p><p>DNA in packaged chromatin is inaccessible to interaction with other</p><p>importante DNA-binding proteins</p><p>45unstructured histone tails are not packed into the folded histone domains</p><p>Chromatin remodeling</p><p>Covalent modifications of histones</p><p>46</p><p>Reversible modifications of the N-terminal:</p><p>• acetylation of lysine by histone</p><p>acetyltransferase (HAT)</p><p>• methylation of lysine and arginine by</p><p>methyltranferases</p><p>• phosphorylation of serine and histidine by</p><p>kinases</p><p>Ubiquitylation of the C-terminal:</p><p>• Nucleosome remodeling</p><p>Chromosomes</p><p>47</p><p>each eukaryotic chromosome is a long single non-uniform chromatin fiber</p><p>Banding patterns of chromatin</p><p>euchromatin – uncoiled</p><p>heterochromatin – condensed (e.g. Y chromosome, Bar body)</p><p>48C-bands (centromeres) in human chromosomes</p><p>Banding patterns of chromatin</p><p>euchromatin – uncoiled</p><p>heterochromatin – condensed (e.g. Y chromosome, Bar body)</p><p>49</p><p>C-bands (centromeres) in mouse (a) and human (b) chromosomes</p><p>(a) (b)</p><p>Banding patterns of chromatin</p><p>50G-bands in human chromosomes</p><p>Visible cytogenetic markers</p><p>51</p><p>Visible cytogenetic markers</p>