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    "text": "General Biology\nWikibooks.org"
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    "text": "March 15, 2013\nOn the 28th of April 2012 the contents of the English as well as German Wikibooks and Wikipedia\nprojects were licensed under Creative Commons Attribution-ShareAlike 3.0 Unported license. An\nURI to this license is given in the list of figures on page 175. If this document is a derived work\nfrom the contents of one of these projects and the content was still licensed by the project under\nthis license at the time of derivation this document has to be licensed under the same, a similar or a\ncompatiblelicense,asstatedinsection4bofthelicense. Thelistofcontributorsisincludedinchapter\nContributors on page 169. The licenses GPL, LGPL and GFDL are included in chapter Licenses on\npage 179, since this book and/or parts of it may or may not be licensed under one or more of these\nlicenses, and thus require inclusion of these licenses. The licenses of the figures are given in the list of\nfigures on page 175. This PDF was generated by the LATEX typesetting software. The LATEX source"
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    "text": "ses, and thus require inclusion of these licenses. The licenses of the figures are given in the list of\nfigures on page 175. This PDF was generated by the LATEX typesetting software. The LATEX source\ncode is included as an attachment (source.7z.txt) in this PDF file. To extract the source from the\nPDF file, we recommend the use of http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/\nutility or clicking the paper clip attachment symbol on the lower left of your PDF Viewer, selecting\nSave Attachment. After extracting it from the PDF file you have to rename it to source.7z. To\nuncompress the resulting archive we recommend the use of http://www.7-zip.org/. The LATEX\nsource itself was generated by a program written by Dirk Hünniger, which is freely available under\nan open source license from http://de.wikibooks.org/wiki/Benutzer:Dirk_Huenniger/wb2pdf.\nThis distribution also contains a configured version of the pdflatex compiler with all necessary"
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    "text": "ailable under\nan open source license from http://de.wikibooks.org/wiki/Benutzer:Dirk_Huenniger/wb2pdf.\nThis distribution also contains a configured version of the pdflatex compiler with all necessary\npackages and fonts needed to compile the LATEX source included in this PDF file."
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    "text": "Contents\n1 Getting Started 3\n2 Biology - The Life Science 5\n2.1 Characteristics of life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5\n2.2 Nature of science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6\n2.3 Scientific method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6\n2.4 Charles Darwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9\n2.5 After Darwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9\n2.6 Challenges to Darwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10\n3 The Nature of Molecules 11\n3.1 Matter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11\n3.2 The atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11\n3.3 Mass and isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12\n3.4 Electrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12\n3.5 Chemical bonds . . . . ."
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    "text": "Mass and isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12\n3.4 Electrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12\n3.5 Chemical bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13\n3.6 Chemical reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13\n3.7 Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13\n4 The Chemical Building Blocks of Life 15\n4.1 Carbon. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15\n4.2 Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15\n4.3 Stereoisomers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16\n4.4 Lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16\n4.5 Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16\n4.6 Hereditary (Genetic) information . . . . . . . . . . . . . . . . . . ."
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    "text": ". . . . . . . . . . . . . . . . 16\n4.5 Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16\n4.6 Hereditary (Genetic) information . . . . . . . . . . . . . . . . . . . . . . . 18\n5 Life: History and Origin 19\n5.1 Properties of life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19\n5.2 Origin of life: 3 hypotheses . . . . . . . . . . . . . . . . . . . . . . . . . . 19\n5.3 The early earth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20\n5.4 Origin of cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21\n5.5 The RNA world? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21\n5.6 The earliest cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21\n5.7 Major steps in evolution of life . . . . . . . . . . . . . . . . . . . . . . . . 22\n6 Cells 23\n7 Cell structure 25\n7.1 What is a cell? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25"
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    "text": "r steps in evolution of life . . . . . . . . . . . . . . . . . . . . . . . . 22\n6 Cells 23\n7 Cell structure 25\n7.1 What is a cell? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25\n7.2 History of cell knowledge . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29\nIII"
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    "text": "Contents\n7.3 Microscopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30\n7.4 Cell size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30\n8 Structure of Eukaryotic cells 31\n8.1 Structure of the nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31\n8.2 Chromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32\n8.3 Endoplasmic reticulum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32\n8.4 The Golgi apparatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34\n8.5 Ribosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34\n8.6 DNA-containing organelles . . . . . . . . . . . . . . . . . . . . . . . . . . . 34\n8.7 Cytoskeleton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35\n9 Membranes 37\n9.1 Biological membranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37\n9.2 Phospholipid . . . . . . . . . . . . . . . . . . . . ."
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    "text": ". . . . . . . . . . . . . . . . . . . 35\n9 Membranes 37\n9.1 Biological membranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37\n9.2 Phospholipid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38\n9.3 Fluid mosaic model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38\n9.4 Membrane proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38\n9.5 Receptor-mediated endocytosis . . . . . . . . . . . . . . . . . . . . . . . . 40\n10 Cell-cell interactions 41\n10.1 Cell signaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41\n10.2 Communicating junctions . . . . . . . . . . . . . . . . . . . . . . . . . . . 42\n11 Energy and Metabolism 43\n11.1 Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43\n11.2 Oxidation–Reduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43\n11.3 NAD+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44"
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    "text": ". . . . . . . . . . 43\n11.2 Oxidation–Reduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43\n11.3 NAD+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44\n11.4 Free energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44\n11.5 Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44\n11.6 ATP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46\n11.7 Biochemical pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46\n12 Respiration: harvesting of energy 47\n12.1 Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47\n12.2 Respiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47\n12.3 Respiration of glucose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47\n12.4 Alternative anaerobic respiration . . . . . . . . . . . . . . . . . . . . . . . 47\n12.5 Glycolysis overview . . . . . . . . . ."
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    "text": "lucose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47\n12.4 Alternative anaerobic respiration . . . . . . . . . . . . . . . . . . . . . . . 47\n12.5 Glycolysis overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48\n12.6 Regeneration of NAD+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48\n12.7 Alcohol fermentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48\n12.8 Lactate formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48\n12.9 Krebs cycle: overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49\n12.10 ATP production. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49\n12.11 Evolution of aerobic respiration . . . . . . . . . . . . . . . . . . . . . . . . 49\n13 Photosynthesis 51\n13.1 Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51\n13.2 “Dark” reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53"
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    "text": "13 Photosynthesis 51\n13.1 Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51\n13.2 “Dark” reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53\n13.3 Prokaryote cell division . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53\nIV"
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    "text": "Contents\n13.4 Bacterial DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . 54\n13.5 Chromosome number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54\n13.6 Eukaryotic chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54\n13.7 Chromosome organization . . . . . . . . . . . . . . . . . . . . . . . . . . . 55\n13.8 Human karyotype stained by chromosome painting . . . . . . . . . . . . . 55\n13.9 Chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55\n13.10 Human chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55\n13.11 Mitotic cell cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55\n13.12 Replicated human chromosomes . . . . . . . . . . . . . . . . . . . . . . . . 56\n13.13 Mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56\n13.14 Plant mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56"
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    "text": ". . . . . . 56\n13.13 Mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56\n13.14 Plant mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56\n13.15 Controlling the cell cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56\n13.16 Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57\n13.17 Mutations and cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57\n14 Sexual reproduction 59\n14.1 Sexual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59\n14.2 Sexual life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59\n14.3 Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59\n14.4 Prophase I: synapsis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.5 Crossing over . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.6 Microtubules and anaphase I . . . . . . ."
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    "text": ". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.5 Crossing over . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.6 Microtubules and anaphase I . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.7 Meiosis II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.8 Evolution of sex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60\n14.9 Consequences of sex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61\n15 Genetics 63\n16 Gregor Mendel and biological inheritance 65\n16.1 Mendel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65\n16.2 Mendel’s experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66\n16.3 Mendel’s seven pairs of traits . . . . . . . . . . . . . . . . . . . . . . . . . 66\n16.4 Locus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66\n16.5 Modern Y chromosome . . . . . . . . . . . . . . . . . . . . . ."
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    "text": ". . . . . . . . . . . . . . . . . . . 66\n16.4 Locus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66\n16.5 Modern Y chromosome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67\n16.6 Chromosome phenomena . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67\n16.7 X-chromosome inactivation . . . . . . . . . . . . . . . . . . . . . . . . . . 67\n16.8 Barr body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67\n16.9 Human genetic disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67\n17 DNA: The Genetic Material 69\n17.1 DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69\n17.2 Historical perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69\n17.3 Hershey-Chase Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . 69\n17.4 DNA/RNA components . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70\n17.5 Chemical structure of DNA . . . . . . . . . ."
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    "text": "Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . 69\n17.4 DNA/RNA components . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70\n17.5 Chemical structure of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . 70\n17.6 3D structure of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70\n17.7 Franklin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70\n17.8 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71\nV"
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    "text": "Contents\n17.9 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71\n17.10 DNA polymerases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71\n17.11 DNA replication complex . . . . . . . . . . . . . . . . . . . . . . . . . . . 72\n17.12 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72\n17.13 DNA replication fork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72\n17.14 Replication units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72\n17.15 Replicon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72\n17.16 What is gene? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72\n18 Gene expression 75\n18.1 “Central Dogma” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75\n18.2 The Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75\n18.3 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."
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    "text": ". . . . . . . . . . . . . . . . . 75\n18.2 The Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75\n18.3 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75\n18.4 Transcription bubble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76\n18.5 Eukaryote mRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76\n18.6 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76\n18.7 Translation in bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76\n18.8 Aminoacyl tRNA synthase . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.9 Ribosome structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.10 Large ribosome subunit . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.11 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.12 Initiation complex . . . . . . . . . . . . . . . . . . . . . . . . ."
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    "page": 6,
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    "text": ". . . . . . . . . . . . . . . . 77\n18.11 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.12 Initiation complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.13 Elongation, translocation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n18.14 Introns/exons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77\n19 Gene regulation 79\n19.1 Transcriptional control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79\n19.2 DNA grooves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79\n19.3 Regulatory proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80\n19.4 Lac operon of E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80\n19.5 Alternative splicing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80\n20 Mutation 81\n20.1 Point Mutations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81\n20.2 Substitution . . . . ."
  },
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    "chunk_id": 21,
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    "page": 6,
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    "text": "ing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80\n20 Mutation 81\n20.1 Point Mutations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81\n20.2 Substitution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81\n20.3 Larger mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82\n20.4 Chromosomal mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82\n20.5 Causes of mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82\n20.6 Effects of mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82\n20.7 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83\n20.8 Original notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83\n20.9 Point mutation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84\n20.10 Acquisition of genetic variability . . . . . . . . . . . . . . . . . . . . . . . 84"
  },
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    "chunk_id": 22,
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    "page": 6,
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    "text": ". . . . . . . . . 83\n20.9 Point mutation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84\n20.10 Acquisition of genetic variability . . . . . . . . . . . . . . . . . . . . . . . 84\n20.11 Eukaryote genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84\n20.12 Barbara McClintock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85\n21 Recombinant DNA technology 87\n21.1 Recombinant DNA technology . . . . . . . . . . . . . . . . . . . . . . . . . 87\nVI"
  },
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    "text": "Contents\n21.2 Restriction endonucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . 87\n21.3 Restriction endonucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . 88\n21.4 Uses of cloned gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88\n21.5 Other molecular procedures . . . . . . . . . . . . . . . . . . . . . . . . . . 88\n21.6 RFLP(restriction fragment length polymorphism) analysis . . . . . . . . . 89\n21.7 Sanger DNA sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89\n21.8 Automated sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89\n21.9 Genome projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89\n21.10 Biochips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90\n21.11 DNA chip controversies . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90\n21.12 Gene patenting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90\n21.13 Stem cells . . . ."
  },
  {
    "chunk_id": 24,
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    "page": 7,
    "chunk_index_in_page": 1,
    "text": ".11 DNA chip controversies . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90\n21.12 Gene patenting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90\n21.13 Stem cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91\n22 Classification of Living Things 93\n22.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97\n22.2 Viral Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98\n22.3 Viral Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99\n22.4 Viruses Practice Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . 99\n22.5 Archaea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100\n22.6 Prokaryote evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100\n22.7 Domains of life: characteristics . . . . . . . . . . . . . . . . . . . . . . . . 101\n22.8 Introduction . . . . . . . . . . . . . . . . . . . . . . ."
  },
  {
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    "page": 7,
    "chunk_index_in_page": 2,
    "text": ". . . . . . . . . . . . . . . . . . . . . 100\n22.7 Domains of life: characteristics . . . . . . . . . . . . . . . . . . . . . . . . 101\n22.8 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101\n22.9 Classification of Protists . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101\n22.10 Protozoa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101\n22.11 Algae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102\n22.12 Slime molds & Water molds . . . . . . . . . . . . . . . . . . . . . . . . . . 103\n22.13 Protists Practice Questions . . . . . . . . . . . . . . . . . . . . . . . . . . 104\n23 Multicellular Photosynthetic Autotrophs 107\n23.1 Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107\n23.2 Plant phyla . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107\n23.3 Plant evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."
  },
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    "page": 7,
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    "text": ". . . . . . . . . . . 107\n23.2 Plant phyla . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107\n23.3 Plant evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107\n23.4 Plant phylogeny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108\n23.5 Plant life cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108\n23.6 Moss life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108\n23.7 Vascular plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108\n23.8 Vascular plant life cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109\n23.9 Pterophyta (ferns) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109\n23.10 Non-seed plants, continued . . . . . . . . . . . . . . . . . . . . . . . . . . . 109\n23.11 Seed plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109\n23.12 Sporophyte/gametophyte . . . . . . . . . . . . . ."
  },
  {
    "chunk_id": 27,
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    "page": 7,
    "chunk_index_in_page": 4,
    "text": ". . . . . . . . . . . . . . . . . . . . . . . . 109\n23.11 Seed plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109\n23.12 Sporophyte/gametophyte . . . . . . . . . . . . . . . . . . . . . . . . . . . 110\n23.13 Megasporangium (nucellus) . . . . . . . . . . . . . . . . . . . . . . . . . . 110\n23.14 Pollen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110\n23.15 Gymnosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110\n23.16 Pine life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110\n23.17 Other Coniferophyta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110\n23.18 Other gymnosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111\n23.19 Angiosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111\nVII"
  },
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    "text": "Contents\n23.20 Earliest angiosperm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111\n23.21 Angiosperm flower . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111\n23.22 Angiosperm life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111\n23.23 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111\n23.24 Nutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112\n23.25 Fungal Reproduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112\n23.26 Types of Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113\n23.27 Key Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114\n23.28 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114\n23.29 Characteristics of an Animal . . . . . . . . . . . . . . . . . . . . . . . . . . 114\n23.30 Introduction to animal phyla . . . . . . . . . . . . . . . . . . . ."
  },
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    "text": ". . . . . . . . . . . . . . . 114\n23.29 Characteristics of an Animal . . . . . . . . . . . . . . . . . . . . . . . . . . 114\n23.30 Introduction to animal phyla . . . . . . . . . . . . . . . . . . . . . . . . . 116\n23.31 Phylum Porifera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117\n23.32 Phylum Cnidaria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118\n23.33 Phylum Platyhelminthes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120\n23.34 Phylum Rotifera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121\n23.35 Phylum Nematoda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121\n23.36 Phylum Annelida . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122\n23.37 Phylum Arthropoda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123\n23.38 Phylum Mollusca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124\n23.39 Phylum Echinodermata . . . . . . . . . . . . . . . . . . . . ."
  },
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    "page": 8,
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    "text": ". . . . . . . . . . . . . . . . . . . 123\n23.38 Phylum Mollusca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124\n23.39 Phylum Echinodermata . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124\n23.40 Phylum Chordata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125\n24 Chordates 127\n24.1 Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127\n24.2 Subphylum Urochordata . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127\n24.3 Subphylum Cephalochordata . . . . . . . . . . . . . . . . . . . . . . . . . 128\n24.4 Subphylum Vertebrata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128\n25 Tissues and Systems 135\n26 Epithelial tissue 137\n27 Connective tissue 139\n28 Muscle tissue 143\n29 Vertebrate digestive system 147\n30 Circulatory system 151\n31 Respiratory system 155\n31.1 Neuron structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156\n31.2 Central nervous system . . . . . . . . . ."
  },
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    "chunk_id": 31,
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    "text": "system 147\n30 Circulatory system 151\n31 Respiratory system 155\n31.1 Neuron structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156\n31.2 Central nervous system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157\n31.3 Peripheral nervous system . . . . . . . . . . . . . . . . . . . . . . . . . . . 157\n32 Sensory systems 159\n32.1 Taste and smell (chemoreception) . . . . . . . . . . . . . . . . . . . . . . . 159\n32.2 Response to gravity and movement . . . . . . . . . . . . . . . . . . . . . . 159\n32.3 Vision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160\nVIII"
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    "text": "Contents\n32.4 Homeostasis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160\n32.5 Osmotic environments and regulations . . . . . . . . . . . . . . . . . . . . 161\n33 Additional material 165\n33.1 External Links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166\n34 Glossary 167\n34.1 Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168\n35 Contributors 169\nList of Figures 175\n36 Licenses 179\n36.1 GNU GENERAL PUBLIC LICENSE . . . . . . . . . . . . . . . . . . . . 179\n36.2 GNU Free Documentation License . . . . . . . . . . . . . . . . . . . . . . 180\n36.3 GNU Lesser General Public License . . . . . . . . . . . . . . . . . . . . . . 181\n1"
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    "text": "1 Getting Started\n3"
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    "chunk_index_in_page": 0,
    "text": "2 Biology - The Life Science\nThe word biology means, \"the science of life\", from the Greek bios, life, and logos, word\nor knowledge. Therefore, Biology is the science of Living Things. That is why Biology is\nsometimes known as Life Science.\nThe science has been divided into many subdisciplines, such as botany1, bacteriology,\nanatomy2, zoology, histology, mycology, embryology, parasitology, genetics3, molecular biol-\nogy4, systematics, immunology, microbiology5, physiology, cell biology6, cytology, ecology7,\nand virology. Other branches of science include or are comprised in part of biology studies,\nincluding paleontology8, taxonomy, evolution, phycology, helimentology, protozoology, en-\ntomology, biochemistry, biophysics, biomathematics, bio engineering, bio climatology and\nanthropology.\n2.1 Characteristics of life\nNot all scientists agree on the definition of just what makes up life. Various characteristics\ndescribe most living things."
  },
  {
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    "page": 13,
    "chunk_index_in_page": 1,
    "text": "o engineering, bio climatology and\nanthropology.\n2.1 Characteristics of life\nNot all scientists agree on the definition of just what makes up life. Various characteristics\ndescribe most living things. However, with most of the characteristics listed below we can\nthink of one or more examples that would seem to break the rule, with something nonliving\nbeing classified as living or something living classified as nonliving. Therefore we are careful\nnot to be too dogmatic in our attempt to explain which things are living or nonliving.\n• Living things are composed of matter structured in an orderly way where simple\nmolecules are ordered together into much larger macromolecules.\nAn easy way to remember this is GRIMNERD C All organisms; - Grow, Respire, Interact,\nMove, Need Nutrients, Excrete (Waste), Reproduce,Death, Cells (Made of)\n• Living things are sensitive, meaning they are able to respond to stimuli.\n• Living things are able to grow, develop, and reproduce."
  },
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    "page": 13,
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    "text": "Need Nutrients, Excrete (Waste), Reproduce,Death, Cells (Made of)\n• Living things are sensitive, meaning they are able to respond to stimuli.\n• Living things are able to grow, develop, and reproduce.\n• Living things are able to adapt over time by the process of natural selection.\n• All known living things use the hereditary molecule, DNA9.\n1 http://en.wikibooks.org/wiki/botany\n2 http://en.wikibooks.org/wiki/anatomy\n3 http://en.wikibooks.org/wiki/genetics\n4 http://en.wikibooks.org/wiki/Molecular%20Biology\n5 http://en.wikibooks.org/wiki/microbiology\n6 http://en.wikibooks.org/wiki/Cell%20Biology\n7 http://en.wikibooks.org/wiki/ecology\n8 http://en.wikibooks.org/wiki/paleontology\n9 http://en.wikipedia.org/wiki/DNA\n5"
  },
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    "text": "Biology - The Life Science\n• Internal functions are coordinated and regulated so that the internal environment of a\nliving thing is relatively constant, referred to as homeostasis10.\nLiving things are organized in the microscopic level from atoms up to cells11. Atoms are\narranged into molecules, then into macromolecules12, which make up organelles13, which\nwork together to form cells. Beyond this, cells are organized in higher levels to form entire\nmulticellular organisms. Cells together form tissues14, which make up organs, which are\npart of organ systems, which work together to form an entire organism. Of course, beyond\nthis, organisms form populations which make up parts of an ecosystem. All of the Earth's\necosystems together form the diverse environment that is the earth.\nExample:-\nsub atoms, atoms, molecules, cells, tissues, organs, organ systems, organisms, population,\ncommunity, eco systems\n2.2 Nature of science\nScience is a methodology for learning about the world."
  },
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    "page": 14,
    "chunk_index_in_page": 1,
    "text": "Example:-\nsub atoms, atoms, molecules, cells, tissues, organs, organ systems, organisms, population,\ncommunity, eco systems\n2.2 Nature of science\nScience is a methodology for learning about the world. It involves the application\nof knowledge.\nThe scientific method deals with systematic investigation, reproducible results, the\nformation and testing of hypotheses, and reasoning.\nReasoning can be broken down into two categories, induction (specific data is used to\ndevelop a generalized observation or conclusion) and deduction (general information leads\nto specific conclusion). Most reasoning in science is done through induction.\nScience as we now know it arose as a discipline in the 17th century.\n2.3 Scientific method\nThe scientific method is not a step by step, linear process. It is an intuitive process, a\nmethodology for learning about the world through the application of knowledge. Scientists\nmust be able to have an \"imaginative preconception\" of what the truth is. Scientists will"
  },
  {
    "chunk_id": 39,
    "source_file": "GeneralBiology.pdf",
    "page": 14,
    "chunk_index_in_page": 2,
    "text": "ntuitive process, a\nmethodology for learning about the world through the application of knowledge. Scientists\nmust be able to have an \"imaginative preconception\" of what the truth is. Scientists will\noften observe and then hypothesize the reason why a phenomenon occurred. They use all\nof their knowledge and a bit of imagination, all in an attempt to uncover something that\nmight be true. A typical scientific investigation might go like so:\nYouobservethataroomappearsdark, andyouponderwhytheroomisdark. Inanattempt\nto find explanations to this curiosity, your mind unravels several different hypotheses. One\nhypothesis might state that the lights are turned off. Another hunch might be that the\nroom's lightbulb has burnt out. Worst yet, you could be going blind. To discover the truth,\n10 http://en.wikipedia.org/wiki/homeostasis\n11 http://en.wikipedia.org/wiki/cell\n12 http://en.wikipedia.org/wiki/macromolecule\n13 http://en.wikipedia.org/wiki/organelle"
  },
  {
    "chunk_id": 40,
    "source_file": "GeneralBiology.pdf",
    "page": 14,
    "chunk_index_in_page": 3,
    "text": "blind. To discover the truth,\n10 http://en.wikipedia.org/wiki/homeostasis\n11 http://en.wikipedia.org/wiki/cell\n12 http://en.wikipedia.org/wiki/macromolecule\n13 http://en.wikipedia.org/wiki/organelle\n14 http://en.wikibooks.org/wiki/General%20Biology%2FTissues\n6"
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    "page": 15,
    "chunk_index_in_page": 0,
    "text": "Scientific method\nyou experiment. You feel your way around the room and find a light switch and turn it on.\nNo light. You repeat the experiment, flicking the switch back and forth. Still nothing. That\nmeans your initial hypothesis, the room is dark because the lights are off, has been rejected.\nYou devise more experiments to test your hypotheses, utilizing a flashlight to prove that\nyou are indeed not blind. In order to accept your last remaining hypothesis as the truth,\nyou could predict that changing the light bulb will fix the problem. If all your predictions\nsucceed, the original hypothesis is valid and is accepted. In some cases, however, your\npredictions will not occur, in which you'll have to start over. Perhaps the power is off.\nFigure 1 How Science is Done\nA diagram that illustrates scientific investigation\nScientists first make observations that raise a particular question. In order to explain the"
  },
  {
    "chunk_id": 42,
    "source_file": "GeneralBiology.pdf",
    "page": 15,
    "chunk_index_in_page": 1,
    "text": "Perhaps the power is off.\nFigure 1 How Science is Done\nA diagram that illustrates scientific investigation\nScientists first make observations that raise a particular question. In order to explain the\nobserved phenomenon, they develop a number of possible explanations, or hypotheses. This\nis the inductive part of science, observing and constructing plausible arguments for why\n7"
  },
  {
    "chunk_id": 43,
    "source_file": "GeneralBiology.pdf",
    "page": 16,
    "chunk_index_in_page": 0,
    "text": "Biology - The Life Science\nan event occurred. Experiments are then used to eliminate one of more of the possible\nhypotheses until one hypothesis remains. Using deduction, scientists use the principles of\ntheir hypothesis to make predictions, and then test to make sure that their predictions are\nconfirmed. After many trials (repeatability) and all predictions have been confirmed, the\nhypothesis then may become a theory.\nQuick Definitions\nObservation - Quantitative and qualitative measurements of the world.\nInference - Deriving new knowledge based upon old knowledge.\nHypotheses - A suggested explanation.\nRejected Hypothesis - An explanation that has been ruled out through experimentation.\nAccepted Hypothesis - An explanation that has not been ruled out through excessive\nexperimentation and makes verifiable predictions that are true.\nExperiment - A test that is used to rule out a hypothesis or validate something already\nknown.\nScientific Method - The process of scientific investigation."
  },
  {
    "chunk_id": 44,
    "source_file": "GeneralBiology.pdf",
    "page": 16,
    "chunk_index_in_page": 1,
    "text": "makes verifiable predictions that are true.\nExperiment - A test that is used to rule out a hypothesis or validate something already\nknown.\nScientific Method - The process of scientific investigation.\nTheory - A widely accepted hypothesis that stands the test of time. Often tested, and\nusually never rejected.\nThe scientific method is based primarily on the testing of hypotheses by experimentation.\nThis involves a control, or subject that does not undergo the process in question. A scientist\nwill also seek to limit variables to one or another very small number, single or minimum\nnumber of variables. The procedure is to form a hypothesis or prediction about what you\nbelieve or expect to see and then do everything you can to violate that, or falsify the\nhypotheses. Although this may seem unintuitive, the process serves to establish more firmly\nwhat is and what is not true.\nA founding principle in science is a lack of absolute truth: the accepted explanation is the"
  },
  {
    "chunk_id": 45,
    "source_file": "GeneralBiology.pdf",
    "page": 16,
    "chunk_index_in_page": 2,
    "text": "hough this may seem unintuitive, the process serves to establish more firmly\nwhat is and what is not true.\nA founding principle in science is a lack of absolute truth: the accepted explanation is the\nmost likely and is the basis for further hypotheses as well as for falsification. All knowledge\nhas its relative uncertainty.\nTheories are hypotheses which have withstood repeated attempts at falsification. Common\ntheories include evolution by natural selection and the idea that all organisms consist of\ncells. The scientific community asserts that much more evidence supports these two ideas\nthan contradicts them.\n8"
  },
  {
    "chunk_id": 46,
    "source_file": "GeneralBiology.pdf",
    "page": 17,
    "chunk_index_in_page": 0,
    "text": "Charles Darwin\n2.4 Charles Darwin\nFigure 2\nCharles Darwin is most remembered today for his contribution of the theory of evolution\nthrough natural selection.\nThe seeds of this theory were planted in Darwin's mind through observations made on a\nfive-year voyage through the New World on a ship called the Beagle. There, he studied\nfossils and the geological record, geographic distribution of organisms, the uniqueness and\nrelatedness of island life forms, and the affinity of island forms to mainland forms.\nUpon his return to England, Darwin pondered over his observations and concluded that\nevolution must occur through natural selection. He declined, however, to publish his work\nbecauseofitscontroversialnature. However, whenanotherscientist, Wallace, reachedsimilar\nconclusions, Darwin was convinced to publish his observations in 1859. His hypothesis\nrevolutionized biology and has yet to be falsified by empirical data collected by mainstream\nscientists.\n2.5 After Darwin"
  },
  {
    "chunk_id": 47,
    "source_file": "GeneralBiology.pdf",
    "page": 17,
    "chunk_index_in_page": 1,
    "text": "ons, Darwin was convinced to publish his observations in 1859. His hypothesis\nrevolutionized biology and has yet to be falsified by empirical data collected by mainstream\nscientists.\n2.5 After Darwin\nSince Darwin's day, scientists have amassed a more complete fossil record, including\nmicroorganisms and chemical fossils. These fossils have supported and added subtleties\nto Darwin's theories. However, the age of the Earth is now held to be much older than\nDarwin thought. Researchers have also uncovered some of the preliminary mysteries of\nthe mechanism of heredity as carried out through genetics and DNA, areas unknown to\nDarwin. Another growing area is comparative anatomy including homology and analogy.\nToday we can see a bit of evolutionary history in the development of embryos, as certain\n(although not all) aspects of development recapitulate evolutionary history.\n9"
  },
  {
    "chunk_id": 48,
    "source_file": "GeneralBiology.pdf",
    "page": 18,
    "chunk_index_in_page": 0,
    "text": "Biology - The Life Science\nThe molecular biology15 study of slowly mutating genes reveal considerable evolutionary\nhistory consistent with fossil and anatomical record.\n2.6 Challenges to Darwin\nFigure 3\nDarwin and his theories have been challenged many times in the last 150 years. The\nchallenges have been primarily religious based on a perceived conflict with the preconceived\nnotion of creationism. Many of those who challenge Darwin have been adherents to the\nyoung earth hypothesis that says that the Earth is only some 6000 years old and that all\nspecies were individually created by a god. Some of the proponents of these theories have\nsuggested that chemical and physical laws that exist today were different or nonexistent in\nearlier ages. However, for the most part, these theories are either not scientifically testable\nand fall outside the area of attention of the field of biology, or have been disproved by one\nor more fields of science."
  },
  {
    "chunk_id": 49,
    "source_file": "GeneralBiology.pdf",
    "page": 18,
    "chunk_index_in_page": 1,
    "text": "ever, for the most part, these theories are either not scientifically testable\nand fall outside the area of attention of the field of biology, or have been disproved by one\nor more fields of science.\nThis text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of Cleveland\nState University.\n15 http://en.wikibooks.org/wiki/molecular%20biology\n10"
  },
  {
    "chunk_id": 50,
    "source_file": "GeneralBiology.pdf",
    "page": 19,
    "chunk_index_in_page": 0,
    "text": "3 The Nature of Molecules\n3.1 Matter\nMatter is defined as anything that has mass1 (an amount of matter in an object) and\noccupies space2 (which is measured as volume3).\n• Particles, from smallest to largest\n1. Subatomic particles\n• Electrons4\n• Protons5\n• Neutrons6\n2. Atoms\n3. Molecules\n4. Macromolecules\n• Origin of matter\n1. Big Bang7, about 13.7 billion years ago\n2. Hydrogen8, helium9\n3. Heavier elements formed in suns, super nova\n• Earth's matter predates formation of sun, 4.5 billion years ago\n• All matter consists of atoms, which are composed of : electrons, protons, neutrons\n3.2 The atom\n• Example: Hydrogen\n• The simplest element\n• One proton (+)\n• One electron in orbit (-)\n• Built by adding one proton (and one electron) at a time\n• Number of protons determines atomic number and number of electrons\n• Neutrons\n• Neutral charge\n1 http://en.wikipedia.org/wiki/mass\n2 http://en.wikipedia.org/wiki/space%23Physics\n3 http://en.wikipedia.org/wiki/volume"
  },
  {
    "chunk_id": 51,
    "source_file": "GeneralBiology.pdf",
    "page": 19,
    "chunk_index_in_page": 1,
    "text": "s determines atomic number and number of electrons\n• Neutrons\n• Neutral charge\n1 http://en.wikipedia.org/wiki/mass\n2 http://en.wikipedia.org/wiki/space%23Physics\n3 http://en.wikipedia.org/wiki/volume\n4 http://en.wikipedia.org/wiki/Electrons\n5 http://en.wikipedia.org/wiki/Protons\n6 http://en.wikipedia.org/wiki/Neutrons\n7 http://en.wikipedia.org/wiki/Big%20Bang\n8 http://en.wikipedia.org/wiki/Hydrogen\n9 http://en.wikipedia.org/wiki/Helium\n11"
  },
  {
    "chunk_id": 52,
    "source_file": "GeneralBiology.pdf",
    "page": 20,
    "chunk_index_in_page": 0,
    "text": "The Nature of Molecules\n• Contribute mass\n• May decay\n• Oxygen10\n• 8 protons (mass)\n• 8 electrons\n• 8 neutrons (mass)\n3.3 Mass and isotopes\n• Atomic mass\n• Sum of masses of protons and neutrons\n• Measured in daltons or AMU (Atomic Mass Unit)\n• An AMU is 1/12 the mass of Carbon-12\n• proton ˜1 AMU or dalton\n• 6.024 x 1023 daltons/gram\n• Atoms with same atomic number belong to same element\n• Isotopes\n• Same atomic number but different atomic mass\n• Some are radioactive\n• Uses of isotopes\n• Radioactive: 3H, 14C, 32P, 35S\n• Tracers in biochemical reactions\n• Detection of molecules in recombinant DNA technology (genetic engineering)\n• Half-life: dating of rocks, fossils\n• Non-radioactive (N, C, O)\n• Diet of organisms (including fossils)\n• Biochemical tracers\n3.4 Electrons\n• Negative charge\n• Held in orbit about nucleus by attraction to positively charged nucleus\n• Atom may gain or lose electron, altering charge\n• Cation: loses electron, positive charge\n• Na+"
  },
  {
    "chunk_id": 53,
    "source_file": "GeneralBiology.pdf",
    "page": 20,
    "chunk_index_in_page": 1,
    "text": "Electrons\n• Negative charge\n• Held in orbit about nucleus by attraction to positively charged nucleus\n• Atom may gain or lose electron, altering charge\n• Cation: loses electron, positive charge\n• Na+\n• Anion: gains electron, negative charge\n• Cl-\n• Determine chemical properties of atoms\n• Number\n• Energy level\n10 http://en.wikipedia.org/wiki/Oxygen\n12"
  },
  {
    "chunk_id": 54,
    "source_file": "GeneralBiology.pdf",
    "page": 21,
    "chunk_index_in_page": 0,
    "text": "Chemical bonds\n3.5 Chemical bonds\n• Form molecules\n• Enzymes: make, break, rearrange chemical bonds in living systems\n• Ionic\n• Covalent\n• Sharing of one or more pairs of electrons\n• Called single, double, or triple\n• No net charge (as in ionic bonds)\n• No free electrons\n• Give rise to discrete molecules\n• Hydrogen\n3.6 Chemical reactions\n• Formation and breaking of chemical bonds\n• Shifting arrangement of atoms\n• Reactants -> products\n• Reactions are influenced by:\n• Temperature\n• Concentration of reactants, products\n• Presence of catalysts (enzymes)\n• Oxidation:reduction\n3.7 Water\n• Essential for life\n• ˜75% earth's surface is water\n• Life evolved in water\n• Solvent for many types of solutes\n• High specific heat\n• High polarity\n• Creates a slightly negative Oxygen and a Slightly positive hydrogen\n• allows formation of Hydrogen Bonds\n3.7.1 Hydrogen bonding\n• A type of polar interaction\n• Critical for:\n• Protein structure\n• Enzymatic reactions\n• Movement of water in plant stems"
  },
  {
    "chunk_id": 55,
    "source_file": "GeneralBiology.pdf",
    "page": 21,
    "chunk_index_in_page": 1,
    "text": "ositive hydrogen\n• allows formation of Hydrogen Bonds\n3.7.1 Hydrogen bonding\n• A type of polar interaction\n• Critical for:\n• Protein structure\n• Enzymatic reactions\n• Movement of water in plant stems\n• Weak and transient\n• Powerful cumulative effect\n13"
  },
  {
    "chunk_id": 56,
    "source_file": "GeneralBiology.pdf",
    "page": 22,
    "chunk_index_in_page": 0,
    "text": "The Nature of Molecules\n• Solubility of many compounds\n• Cohesion (capillary action)\n• Lower density of ice\n• Formed between molecules other than water\n• Protein structure\n• DNA11, RNA12 structure\nWater organizes nonpolar molecules\n• Nonpolar molecules: no polarity (+/-) charges\n• Hydrophobic: exclude water because they don't form hydrogen bonds with it\n• Consequences:\n• Membranes\n• Protein structure\n• Hydrophilic: polar substances associate with water\nIonization of water: H O -> H+ + OH-\n2\n• Forms a Hydrogen ion (H+), hydroxide ion (OH-)\n• Due to spontaneous breakage of covalent bond\n• At 25°C, 1 liter of water contains 10-7 moles of H+ ions: 10-7 moles/liter\npH\n• A convenient way of indicating H+ concentration\n• pH13 = -log[H+]\n• For water, pH = -log[10-7] = 7\n• Since for each H+ in pure water, there is one OH-, pH of 7 indicates neutrality\n• Logarithmic scale\nBuffer\n• Reservoir for H+\n• Maintains relatively constant pH over buffering range"
  },
  {
    "chunk_id": 57,
    "source_file": "GeneralBiology.pdf",
    "page": 22,
    "chunk_index_in_page": 1,
    "text": "-log[10-7] = 7\n• Since for each H+ in pure water, there is one OH-, pH of 7 indicates neutrality\n• Logarithmic scale\nBuffer\n• Reservoir for H+\n• Maintains relatively constant pH over buffering range\nThis text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the\nCleveland State University.\n11 http://en.wikipedia.org/wiki/DNA\n12 http://en.wikipedia.org/wiki/RNA\n13 http://en.wikipedia.org/wiki/pH\n14"
  },
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    "page": 23,
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    "text": "4 The Chemical Building Blocks of Life\nBuilding blocks of life\n• Carbon based: organic molecules\n• Carbohydrates: CHO\n• Lipids: CHO, water insoluble\n• Proteins: CHONS, structure/function in cells\n• Nucleic acids: CHONP, hereditary (genetic) information\n4.1 Carbon\n• Can make 4 covalent bonds1\n• Chains\n• Straight\n• Branched\n• Ring\n• Hydrocarbons2 (C, H): store energy\n• Functional groups\n• Attach to carbon\n• Alter chemical properties\n• Form macromolecules\n• Sapoteton\n4.2 Carbohydrates\n• Principally CHO (rare N, S and P)\n• 1C:2H:1O ratio\n• Energy rich (many C-H bonds)\n• Monosaccharides (principal: glucose3)\n• Simple sugars\n• Principle formula: C H O\n6 12 6\n• Form rings in water solution\n• Disaccharides (sucrose, lactose)\n• Polysaccharides (starch, glycogen, cellulose, chitin)\n1 http://en.wikipedia.org/wiki/covalent%20bonds\n2 http://en.wikipedia.org/wiki/Hydrocarbons\n3 http://en.wikipedia.org/wiki/glucose\n15"
  },
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    "page": 24,
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    "text": "The Chemical Building Blocks of Life\n4.3 Stereoisomers\n• Bond angles of carbon point to corners of a tetrahedron\n• When 4 different groups are attached to a carbon, it is asymmetric, leading to various\ntypes of isomerism\n• Stereoisomers: (D, L)\n• Same chemical properties\n• Different biological properties\n• D sugars, L amino acids\n4.4 Lipids\n• C-H bonds (nonpolar) instead of C-OH bonds as in carbohydrates\n• High energy\n• Hydrophobic (insoluble in water)\n• Categories\n• Fats: glycerol and three fatty acids\n• Phospholipids: primary component of membranes\n• Prostaglandins: chemical messengers (hormones)\n• Steroids: membrane component; hormones\n• Terpenes: pigments; structure\n4.4.1 Fatty acids\n• Hydrocarbon chain\n• Even number of C, 14->20\n• Terminates in carboxyl group\n• Saturated: contain maximum number of hydrogens (all single bonds); maximum energy\n• Unsaturated: one or more double bonds\n• Usually higher melting point\n• Many common oils are polyunsaturated\n4.5 Proteins"
  },
  {
    "chunk_id": 60,
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    "page": 24,
    "chunk_index_in_page": 1,
    "text": "ated: contain maximum number of hydrogens (all single bonds); maximum energy\n• Unsaturated: one or more double bonds\n• Usually higher melting point\n• Many common oils are polyunsaturated\n4.5 Proteins\n• Polymer of amino acids\n• 21 different amino acids found in proteins\n• Sequence of amino acids determined by gene\n• Amino acid sequence determines shape of molecule\n• Linked by peptide bond (covalent)\n• Functions\n• regulate chemical reactions and cell processes [enzymes]\n• form bone and muscle; various other tissues\n• facilitate transport across cell membrane [carrier proteins]\n16"
  },
  {
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    "page": 25,
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    "text": "Proteins\n• fight disease [antibodies]\n• Motifs: folding patterns of secondary structure\n• Domains: structural, functional part of protein often independent of another part; often\nencoded by different exons\n• Shape determines protein's function\n4.5.1 Amino acids\n• 21 commonly found in proteins\n• 21st is selenocysteine, not mentioned in text\n• Common structure\n• Amino group: NH\n2\n• Carboxyl group: COOH\n• R group- 4 different kinds of R groups\n• acidic\n• basic\n• hydrophilic (polar)\n• hydrophobic (nonpolar)\n• Confer individual properties on amino acids\n• List of amino acids4\n4.5.2 Structure\n• Primary structure: the amino acid sequence\n• Determines higher orders of structure\n• Critical for structure and function of protein\n• Secondary: stabilized by intramolecular hydrogen bonding\n• helix\n• sheet\n• Tertiary: folding, stabilized by ionic bonds (between R groups), hydrogen bonding, van\nder Waal's forces, hydrophobic interactions\n• Quaternary: _2 polypeptides\n4.5.3 Function"
  },
  {
    "chunk_id": 62,
    "source_file": "GeneralBiology.pdf",
    "page": 25,
    "chunk_index_in_page": 1,
    "text": "nding\n• helix\n• sheet\n• Tertiary: folding, stabilized by ionic bonds (between R groups), hydrogen bonding, van\nder Waal's forces, hydrophobic interactions\n• Quaternary: _2 polypeptides\n4.5.3 Function\n• Requires proper folding, cofactors, pH, temperature, etc.\n• Proteins are often modified after synthesis\n• Chemical modification\n• Addition of heme groups (hemoglobin, cytochrome)\n• Denatured proteins can not function properly\n• Proteins are degraded by proteosome as part of constant turnover of cell components\n4 http://en.wikipedia.org/wiki/Amino%20acid%23List%20of%20amino%20acids\n17"
  },
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    "page": 26,
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    "text": "The Chemical Building Blocks of Life\n4.6 Hereditary (Genetic) information\n• Nucleic acids\n• DNA: deoxyribonucleic acid\n• Hereditary information of all cells\n• Hereditary information for many viruses\n• RNA: ribonucleic acid\n• Hereditary information of certain viruses (HIV5)\n• Intermediate in gene expression\n• Composed of nucleotides\n• Ribonucleotides\n• Deoxyribonucleotides\n4.6.1 RNA DNA origin\n• Which came first?\n• Paradox: DNA encodes protein necessary for its own replication\n• Discovery of catalytic RNA by Cech and Altman suggested that RNA might have been\nfirst self-replicating molecule\n• DNA evolved as more stable type of storage molecule\nThis text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the\nCleveland State University.\nProteins: Their building block is amino acids. The bond connecting 2 of the amino acids\ntogetherarecalledpeptidebonds. Oneofthesebondsmakesamonopeptide, twoadipeptide,\nand any more than that makes a polypeptide."
  },
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    "page": 26,
    "chunk_index_in_page": 1,
    "text": "eir building block is amino acids. The bond connecting 2 of the amino acids\ntogetherarecalledpeptidebonds. Oneofthesebondsmakesamonopeptide, twoadipeptide,\nand any more than that makes a polypeptide.\n5 http://en.wikipedia.org/wiki/HIV\n18"
  },
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    "page": 27,
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    "text": "5 Life: History and Origin\n5.1 Properties of life\n1. Organization: Being structurally composed of one or more cells, which are the basic\nunits of life.\n• prokaryote: no nucleus\n• eukaryote: membrane bound nucleus.\n2. Sensitivity: respond to stimuli.\n3. Energy Processing\n4. Growth and Development\n5. Reproduction\n• hereditary mechanisms to make more of self; DNA based.\n6. Regulation, including homeostasis.\n7. Evolution.\n5.2 Origin of life: 3 hypotheses\n• Extraterrestrial origin (panspermia): meteor, comet borne from elsewhere in universe\n• evidence of amino acids and other organic material in space (but often both D & L\nforms)\n• questionable bacterial fossils in Martian rock\n-However, this would imply that some other origin of life was likely because it would have\nhad to happen elsewhere before it could be transported here, and the only difference would\nbe that life did not originate on Earth.\n• Spontaneous origin on earth: primitive self-replicating macromolecules acted upon by"
  },
  {
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    "page": 27,
    "chunk_index_in_page": 1,
    "text": "here before it could be transported here, and the only difference would\nbe that life did not originate on Earth.\n• Spontaneous origin on earth: primitive self-replicating macromolecules acted upon by\nnatural selection ((macro)Evolution is one example of this)\n-This is often attacked for the seeming impossibility for life to have been produced by a\nchemical reaction triggered by lightning and the ability of any produced DNA to actually be\nin a sequence that could produce a working model of life if replicated. It is also attacked\nfor religious reasons, as it bypasses things like the idea of a supreme being directly creating\nhumans. It also seems unlikely to some that such huge changes are possible in evolution\n19"
  },
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    "page": 28,
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    "text": "Life: History and Origin\nwithout evidence of an \"in-between stage\" that is credible. Many of the stages of man are\ndisputed due to their somewhat shakey grounds. For example, bones from other animals\nhave been taken accidentally in some cases to be part of a humanoid, and complete skeletons\nhave been sketched out from a limited number of bones.\n• Special creation: religious explanations (Intelligent Design is one popular example of\nthis.) These explanations contend that life was created by God (or perhaps some other\nIntelligent Designer).\n• Proponents of Intelligent design suggest that the vast complexity of life could only\nhave been intentionally designed while other creationists cite biblical support.\n-This is often attacked for many of the same reasons that religion is attacked, and is often\nregarded as superstitious and/or unscientific.\n• It is debated as to whether schools should teach one hypothesis or the other when talking\nabout the origin of life."
  },
  {
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    "page": 28,
    "chunk_index_in_page": 1,
    "text": "religion is attacked, and is often\nregarded as superstitious and/or unscientific.\n• It is debated as to whether schools should teach one hypothesis or the other when talking\nabout the origin of life. However, since they are all currently known major hypotheses\n(and sometimes hypotheses proven wrong are shown for educational purposes), this\nwikibook includes what it can without discriminating unfairly against one hypothesis or\nthe other.\n5.3 The early earth\nIt is believed that the Earth was formed about 4.5 billion years ago.\n• Heavy bombardment by rubble ceased about 3.8 billion years ago.\n• Reducing atmosphere: much free H\n• also H O, NH , CH\n2 3 4\n• little, if any, free O\n2\n• with numerous H electrons, require little energy to form organic compounds with C\n• Warm oceans, estimated at 49-88°C\n• Lack of O and consequent ozone (O ) meant considerable UV energy\n2 3\nChemical reactions on early earth\n• UV and other energy sources would promote chemical reactions and formation of organic"
  },
  {
    "chunk_id": 69,
    "source_file": "GeneralBiology.pdf",
    "page": 28,
    "chunk_index_in_page": 2,
    "text": "9-88°C\n• Lack of O and consequent ozone (O ) meant considerable UV energy\n2 3\nChemical reactions on early earth\n• UV and other energy sources would promote chemical reactions and formation of organic\nmolecules\n• Testable hypothesis: Miller-Urey experiment\n• simulated early atmospheric conditions\n• found amino acids, sugars, etc., building blocks of life\n• won Nobel prize for work\n• experiment showed prebiotic synthesis of biological molecules was possible\nIssues\n• Miller later conceded that the conditions in his experiments were not representative of\nwhat is currently thought to be those of early earth\n• He also conceded that science has no answer for how amino acids could self-organize into\nreplicating molecules and cells\n• In the 50 years since Miller-Urey, significant issues and problems for biogenesis have been\nidentified. This is a weak hypothesis at this time.\n20"
  },
  {
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    "page": 29,
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    "text": "Origin of cells\n• Conclusion: Life exists, we don't know why.\n5.4 Origin of cells\nCells are very small and decompose quickly after death. As such, fossils of the earliest cells\ndo not exist. Scientists have had to form a variety of theories on how cells (and hence life)\nwas created on Earth.\n• Bubble hypothesis\n• A. Oparin, J.B.S. Haldane, 1930’s\n• Primary abiogenesis: life as consequence of geochemical processes\n• Protobionts: isolated collections of organic material enclosed in hydrophobic bubbles\n• Numerous variants: microspheres, protocells, protobionts, micelles, liposomes, coacer-\nvates\n• Other surfaces for evolution of life\n• deep sea thermal vents\n• ice crystals\n• clay surfaces\n• tidal pools\n5.5 The RNA world?\n• DNA → RNA → polypeptide (protein)\n• Catalytic RNA: ribozyme\n• discovered independently by Tom Cech and Sid Altman (Nobel prize)\n• catalytic properties: hydrolysis, polymerization, peptide bond formation, etc.\n• Self-replicating RNA molecule may have given rise to life"
  },
  {
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    "page": 29,
    "chunk_index_in_page": 1,
    "text": "red independently by Tom Cech and Sid Altman (Nobel prize)\n• catalytic properties: hydrolysis, polymerization, peptide bond formation, etc.\n• Self-replicating RNA molecule may have given rise to life\n• consistent with numerous roles for RNA in cells as well as roles for ribonucleotides\n(ATP)\n• relationship to bubble-like structures is uncertain\n5.6 The earliest cells\n• Microfossils\n• ˜3.5 by\n• resemble bacteria: prokaryotes\n• biochemical residues\n• stromatolites\n• Archaebacteria (more properly Archaea)\n• extremophiles: salt, acid, alkali, heat, methanogens\n• may not represent most ancient life\n• Eubacteria\n• cyanobacteria: photosynthesis\n• atmospheric O ; limestone deposits\n2\n21"
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  {
    "chunk_id": 72,
    "source_file": "GeneralBiology.pdf",
    "page": 30,
    "chunk_index_in_page": 0,
    "text": "Life: History and Origin\n• chloroplasts of eukaryotes\nCyanobacteria\n5.7 Major steps in evolution of life\n• Prebiotic synthesis of macromolecules\n• Self replication\n• RNA? (primitive metabolism)\n• DNA as hereditary material\n• 1st cells\n• Photosynthesis\n• Aerobic respiration\n• Multicellularity (more than once)\nThis text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the\nCleveland State University.\n22"
  },
  {
    "chunk_id": 73,
    "source_file": "GeneralBiology.pdf",
    "page": 31,
    "chunk_index_in_page": 0,
    "text": "6 Cells\n23"
  },
  {
    "chunk_id": 74,
    "source_file": "GeneralBiology.pdf",
    "page": 33,
    "chunk_index_in_page": 0,
    "text": "7 Cell structure\n7.1 What is a cell?\nThe word cell comes from the Latin word \"cella\", meaning \"small room\", and it was first\ncoined by a microscopist observing the structure of cork. The cell is the basic unit of all\nliving things, and all organisms are composed of one or more cells. Cells are so basic and\ncritical to the study of life, in fact, that they are often referred to as \"the building blocks of\nlife\". Organisms - bacteria, amoebae and yeasts, for example - may consist of as few as one\ncell, while a typical human body contains about a trillion cells.\nAccording to Cell Theory, first proposed by Schleiden and Schwann in 1839, all life consists\nof cells. The theory also states that all cells come from previously living cells, all vital\nfunctions (chemical reactions) of organisms are carried out inside of cells, and that cells\ncontain necessary hereditary information to carry out necessary functions and replicate\nthemselves.\nAll cells contain:"
  },
  {
    "chunk_id": 75,
    "source_file": "GeneralBiology.pdf",
    "page": 33,
    "chunk_index_in_page": 1,
    "text": "chemical reactions) of organisms are carried out inside of cells, and that cells\ncontain necessary hereditary information to carry out necessary functions and replicate\nthemselves.\nAll cells contain:\n• Lipid bilayer boundary (plasma membrane1)\n• Cytoplasm2\n• DNA3 (hereditary information)\n• Ribosomes4 for protein synthesis\nEukaryotic cells also contain:\n• At least one nucleus5\n• Mitochondria6 for cell respiration and energy\nCells may also contain:\n• Lysosomes7\n• Peroxisomes8\n• Vacuoles9\n• Cell walls10\n1 http://en.wikipedia.org/wiki/plasma%20membrane\n2 http://en.wikipedia.org/wiki/Cytoplasm\n3 http://en.wikipedia.org/wiki/DNA\n4 http://en.wikipedia.org/wiki/Ribosome\n5 http://en.wikipedia.org/wiki/Cell%20Nucleus\n6 http://en.wikipedia.org/wiki/Mitochondrion\n7 http://en.wikipedia.org/wiki/Lysosome\n8 http://en.wikipedia.org/wiki/Peroxisome\n9 http://en.wikipedia.org/wiki/Vacuole\n10 http://en.wikipedia.org/wiki/Cell%20Wall\n25"
  },
  {
    "chunk_id": 76,
    "source_file": "GeneralBiology.pdf",
    "page": 34,
    "chunk_index_in_page": 0,
    "text": "Cell structure\n7.1.1 Concepts\nPlasma Membrane\nPhospholipidbilayer,whichcontainsgreatamountofproteins,themostimportantfunctions\nare the following:\n1. It selectively isolates the content of the cell of the external atmosphere.\n2. It regulates the interchange of substances between the cytoplasm and the environment.\n3. Communicates with other cells.\nModel of the fluid mosaic\nDescribes the structure of the plasma membrane, this model was developed in 1972 by\ncellular biologists J. Singer and L. Nicholson.\nPhospholipid bilayer\nIs in the plasma membrane and produces the fluid part of membranes.\nProteins\nLong chains of amino acids.\nGlucose proteins\nProteins together with carbohydrates in the plasma membrane, mostly in the outer parts\nof the cell.\nFunctions of proteins\nTransport oxygen, they are components of hair and nails, and allow the cell interact with\nits environment.\nTransport Proteins\nRegulate the movement of soluble water molecules, through the plasma membrane. Some"
  },
  {
    "chunk_id": 77,
    "source_file": "GeneralBiology.pdf",
    "page": 34,
    "chunk_index_in_page": 1,
    "text": "oxygen, they are components of hair and nails, and allow the cell interact with\nits environment.\nTransport Proteins\nRegulate the movement of soluble water molecules, through the plasma membrane. Some\ntransport proteins called channel proteins form pores or channels in the membrane so\nthat water soluble molecules pass.\nCarrying proteins\nHave union sites that can hold specific molecules.\nReception proteins\nThey activate cellular responses when specific molecules join.\nProteins of recognition\nThey work as identifiers and as place of union to the cellular surface.\nFluid\nIt is any substance that can move or change of form.\nConcentration\nNumber of molecules in a determined unit of volume.\n26"
  },
  {
    "chunk_id": 78,
    "source_file": "GeneralBiology.pdf",
    "page": 35,
    "chunk_index_in_page": 0,
    "text": "What is a cell?\nGradient\nPhysical difference between two regions of space, in such a way that the molecules tend to\nmove in response to the gradients.\nDiffusion\nMovement of the molecules in a fluid, from the regions of high concentration to those of\nlow concentration.\nPassive transport\nMovement of substances in a membrane that doesn’t need to use energy.\nSimple diffusion\nDiffusion of water, gases or molecules across the membrane.\nFacilitated diffusion\nDiffusion of molecules across the membranes with the participation of proteins.\nOsmosis\nDiffusion of the water across a membrane with differential permeability.\nTransport that needs energy\nMovement of substances across a membrane generally in opposition to a gradient of\nconcentration with the requirement of energy.\nActive transport\nMovement of small molecules using energy (ATP).\nEndocytosis\nMovement of big particles towards the interior of the cell using energy. The cells enclose\nparticles or liquids.\nPinocytosis"
  },
  {
    "chunk_id": 79,
    "source_file": "GeneralBiology.pdf",
    "page": 35,
    "chunk_index_in_page": 1,
    "text": "tive transport\nMovement of small molecules using energy (ATP).\nEndocytosis\nMovement of big particles towards the interior of the cell using energy. The cells enclose\nparticles or liquids.\nPinocytosis\n(Literally cell drinking) Form in which the cell introduces liquids.\nPhagocytosis\nWay of eating of the cells. It feeds in this case of big particles or entire microorganisms.\nPseudopods\nFalse feet (the amoeba).\nExocitosis\nMovement of materials out of the cell with the use of energy. It throws waste material.\nIsotonic\nThe cytoplasm fluid of the interior of the cells is the same that the outer.\nHypertonic solution\n27"
  },
  {
    "chunk_id": 80,
    "source_file": "GeneralBiology.pdf",
    "page": 36,
    "chunk_index_in_page": 0,
    "text": "Cell structure\nThe solutions that have a higher concentration of dissolved particles than the cellular\ncytoplasm and that therefore water of the cells goes out with osmosis.\nHypotonic\nThe solutions with a concentration of dissolved particles lower than the cytoplasm of a cell\nand that therefore do that water enters the cell with osmosis.\nSwelling\nPressure of the water inside the vacuole.\nEndoplasmic Reticulum\nIt is the place of the synthesis of the cellular membrane.\n7.1.2 Structure and function of the cell\nRudolf Virchow\nZoologist, who proposed the postulates of the cellular theory, observes that the living cells\ncould grow and be in two places at the same time, he proposed that all the cells come from\nother equal cells and proposed 3 postulates:\n1. Every living organism is formed from one or more cells\n2. The smallest organisms are unicellular and these in turn are the functional units of\nthe multicellular organisms.\n3. All the cells come from preexisting cells."
  },
  {
    "chunk_id": 81,
    "source_file": "GeneralBiology.pdf",
    "page": 36,
    "chunk_index_in_page": 1,
    "text": "ism is formed from one or more cells\n2. The smallest organisms are unicellular and these in turn are the functional units of\nthe multicellular organisms.\n3. All the cells come from preexisting cells.\n7.1.3 Common characteristics of all the cells\nMolecular components\nProteins, amino acids, lipids, sweeten, DNA, RNA.\nStructural components\nPlasmatic membrane, citoplasm, ribosomes.\nRobert Hooke\nHe postuled for the first time the term cell\nProkaryotes\nTheir genetic material is not enclosed in a membrane ex. Bacterias\nEukaryotes\nTheir genetic material is contained inside a nucleus closed by a membrane\n28"
  },
  {
    "chunk_id": 82,
    "source_file": "GeneralBiology.pdf",
    "page": 37,
    "chunk_index_in_page": 0,
    "text": "History of cell knowledge\n7.2 History of cell knowledge\nThe optical microscope was first invented in 17th century. Shortly thereafter scientists began\nto examine living and dead biological tissues in order to better understand the science of\nlife. Some of the most relevant discovery milestones of the time period include:\n• The invention of the microscope11, which allowed scientists for the first time to see\nbiological cells\n• Robert Hooke12 in 1665 looked at cork under a microscope and described what he called\ncork \"cells\"\n• Anton van Leeuwenhoek13 called the single-celled organisms that he saw under the\nmicroscope \"animalcules\"\n• Matthias Jakob Schleiden14, a botanist, in 1838 determined that all plants consist of\ncells\n• Theodor Schwann15, a zoologist, in 1839 determined that all animals consist of cells\n• Rudolf Virchow16 proposed the theory that all cells arise from previously existing cells\nIn 1838, the botanist Matthias Jakob Schleiden and the physiologist Theodor Schwann"
  },
  {
    "chunk_id": 83,
    "source_file": "GeneralBiology.pdf",
    "page": 37,
    "chunk_index_in_page": 1,
    "text": "animals consist of cells\n• Rudolf Virchow16 proposed the theory that all cells arise from previously existing cells\nIn 1838, the botanist Matthias Jakob Schleiden and the physiologist Theodor Schwann\ndiscovered that both plant cells and animal cells had nuclei. Based on their observations,\nthe two scientists conceived of the hypothesis that all living things were composed of cells.\nIn 1839, Schwann published 'Microscopic Investigations on the Accordance in the Structure\nand Growth of Plants and Animals', which contained the first statement of their joint cell\ntheory.\n7.2.1 Cell Theory\nSchleiden and Schwann proposed spontaneous generation as the method for cell origination,\nbut spontaneous generation (also called abiogenesis17) was later disproven. Rudolf Virchow\nfamously stated \"Omnis cellula e cellula\"... \"All cells only arise from pre-existing cells.\" The\nparts of the theory that did not have to do with the origin of cells, however, held up to"
  },
  {
    "chunk_id": 84,
    "source_file": "GeneralBiology.pdf",
    "page": 37,
    "chunk_index_in_page": 2,
    "text": "dolf Virchow\nfamously stated \"Omnis cellula e cellula\"... \"All cells only arise from pre-existing cells.\" The\nparts of the theory that did not have to do with the origin of cells, however, held up to\nscientific scrutiny and are widely agreed upon by the scientific community today.\nThe generally accepted portions of the modern Cell Theory are as follows: (1) The cell is the\nfundamental unit of structure and function in living things. (2) All organisms are made up\nof one or more cells. (3) Cells arise from other cells through cellular division. (4) Cells carry\ngenetic material passed to daughter cells during cellular division. (5) All cells are essentially\nthe same in chemical composition. (6) Energy flow (metabolism and biochemistry) occurs\nwithin cells.\n11 http://en.wikipedia.org/wiki/microscope\n12 http://en.wikipedia.org/wiki/Robert%20Hooke\n13 http://en.wikipedia.org/wiki/Anton%20van%20Leeuwenhoek\n14 http://en.wikipedia.org/wiki/Matthias%20Jakob%20Schleiden"
  },
  {
    "chunk_id": 85,
    "source_file": "GeneralBiology.pdf",
    "page": 37,
    "chunk_index_in_page": 3,
    "text": "/en.wikipedia.org/wiki/microscope\n12 http://en.wikipedia.org/wiki/Robert%20Hooke\n13 http://en.wikipedia.org/wiki/Anton%20van%20Leeuwenhoek\n14 http://en.wikipedia.org/wiki/Matthias%20Jakob%20Schleiden\n15 http://en.wikipedia.org/wiki/Theodor%20Schwann\n16 http://en.wikipedia.org/wiki/Rudolf%20Virchow\n17 http://en.wikipedia.org/wiki/Abiogenesis\n29"
  },
  {
    "chunk_id": 86,
    "source_file": "GeneralBiology.pdf",
    "page": 38,
    "chunk_index_in_page": 0,
    "text": "Cell structure\n7.3 Microscopes\n• Allow greater resolution, can see finer detail\n• Eye: resolution of ˜ 100 μm\n• Light microscope18: resolution of ˜ 200 nm\n• Limited to cells are larger organelles within cells\n• Confocal microscopy19: 2 dimension view\n• Electron microscope20: resolution of ˜0.2 nm\n• Laser tweezers: move cell contents\n7.4 Cell size\nOne may wonder why all cells are so small. If being able to store nutrients is beneficial\nto the cell, how come there are no animals existing in nature with huge cells? Physical\nlimitations prevent this from occurring. A cell must be able to diffuse gases and nutrients in\nand out of the cell. A cell's surface area does not increase as quickly as its volume, and as a\nresult a large cell may require more input of a substance or output of a substance than it\nis reasonably able to perform. Worse, the distance between two points within the cell can\nbe large enough that regions of the cell would have trouble communicating, and it takes a"
  },
  {
    "chunk_id": 87,
    "source_file": "GeneralBiology.pdf",
    "page": 38,
    "chunk_index_in_page": 1,
    "text": "a substance than it\nis reasonably able to perform. Worse, the distance between two points within the cell can\nbe large enough that regions of the cell would have trouble communicating, and it takes a\nrelatively long time for substances to travel across the cell.\nThat is not to say large cells don't exist. They are, once again, less efficient at exchanging\nmaterials within themselves and with their environment, but they are still functional. These\ncells typically have more than one copy of their genetic information, so they can manufacture\nproteins locally within different parts of the cell.\nKey concepts: Cell size:\n• Is limited by need for regions of cell to communicate\n• Diffuse oxygen and other gases\n• Transport of mRNA21 and protein22s\n• Surface area to volume ratio limited\n• Larger cells typically:\n• Have extra copies of genetic information\n• Have slower communication between parts of cell\n18 http://en.wikipedia.org/wiki/Light%20microscope"
  },
  {
    "chunk_id": 88,
    "source_file": "GeneralBiology.pdf",
    "page": 38,
    "chunk_index_in_page": 2,
    "text": "area to volume ratio limited\n• Larger cells typically:\n• Have extra copies of genetic information\n• Have slower communication between parts of cell\n18 http://en.wikipedia.org/wiki/Light%20microscope\n19 http://en.wikipedia.org/wiki/microscopy\n20 http://en.wikipedia.org/wiki/Electron%20microscope\n21 http://en.wikipedia.org/wiki/RNA\n22 http://en.wikipedia.org/wiki/protein\n30"
  },
  {
    "chunk_id": 89,
    "source_file": "GeneralBiology.pdf",
    "page": 39,
    "chunk_index_in_page": 0,
    "text": "8 Structure of Eukaryotic cells\nEukaryotic1 cells feature membrane delimited nucleii containing two or more linear chromo-\nsome2s; numerous membrane-bound cytoplasmic organelles: mitochondria, RER3, SER4,\nlysosomes, vacuole5s, chloroplast6s; ribosomes and a cytoskeleton7. Also, plants, fungi, and\nsome protists have a cell wall.\n8.1 Structure of the nucleus\nThe nucleus is the round object in the cell that holds the genetic information (DNA) of the\ncell. It is surrounded by a nuclear envelope and has a nucleolus inside.\n8.1.1 Nuclear envelope\nThenuclearenvelopeisadouble-layeredplasmamembrane8 likethecellmembrane, although\nwithout membrane proteins. To allow some chemicals to enter the nucleus, the nuclear\nenvelope has structures called Nuclear pore9s. The nuclear envelope is continuous with the\nendoplasmic reticulum.\n8.1.2 Nucleolus\nThe nucleolus appears in a microscope as a small dark area within the nucleus. The nucleolus"
  },
  {
    "chunk_id": 90,
    "source_file": "GeneralBiology.pdf",
    "page": 39,
    "chunk_index_in_page": 1,
    "text": "called Nuclear pore9s. The nuclear envelope is continuous with the\nendoplasmic reticulum.\n8.1.2 Nucleolus\nThe nucleolus appears in a microscope as a small dark area within the nucleus. The nucleolus\nis the area where there is a high amount of DNA transcription10 taking place.\n1 http://en.wikipedia.org/wiki/Eukaryote\n2 http://en.wikipedia.org/wiki/chromosome\n3 http://en.wikipedia.org/wiki/RER\n4 http://en.wikipedia.org/wiki/SER\n5 http://en.wikipedia.org/wiki/vacuole\n6 http://en.wikipedia.org/wiki/chloroplast\n7 http://en.wikipedia.org/wiki/cytoskeleton\n8 http://en.wikibooks.org/wiki/Plasma%20membrane\n9 http://en.wikibooks.org/wiki/Nuclear%20pore\n10 http://en.wikibooks.org/wiki/DNA%20transcription\n31"
  },
  {
    "chunk_id": 91,
    "source_file": "GeneralBiology.pdf",
    "page": 40,
    "chunk_index_in_page": 0,
    "text": "Structure of Eukaryotic cells\n8.2 Chromatin\nChromosomes consist of chromatin11. This is made up of strings of DNA, which typically\nmeasure centimeters in length if stretched out. This DNA is wound around a histone12 core\nand organized into nucleosome13s.\nThe chromatin14 must be uncoiled for gene expression15 and replication16. Chromosome\nmicrograph\n8.3 Endoplasmic reticulum\nThe endoplasmic reticulum17 is a cellular organelle18 made up of a series of extended folded\nintracellular membranes. It is continuous with the nuclear membane.\nThere are two main types of endoplasmic reticulum:\n• RER: rough endoplasmic reticulum (site of protein synthesis19) associated with ribosomes\n• SER: smooth endoplasmic reticulum (site of lipid synthesis20)\n8.3.1 Rough Endoplasmic Reticulum\nProteins are directed to the RER by a signal sequence of a growing polypeptide21s on\nthe ribosome. This is recognised by a signal recognition particle which brings the ribo-"
  },
  {
    "chunk_id": 92,
    "source_file": "GeneralBiology.pdf",
    "page": 40,
    "chunk_index_in_page": 1,
    "text": "ugh Endoplasmic Reticulum\nProteins are directed to the RER by a signal sequence of a growing polypeptide21s on\nthe ribosome. This is recognised by a signal recognition particle which brings the ribo-\nsome/polypeptide complex to a channel on the RER called a translocon. At the translocon,\nthe signal sequence and ribosome/polypeptide complex interact with the translocon to open\nit. The signal sequence becomes attached to the translocon. The ribosome can continue to\ntranslate the polypeptide into the lumen of the RER. As synthesis continues, 2 processes\ncan happen.\n1. If the protein is destined to become a membrane bound protein then the protein\nsynthesis will continue until termination. The ribosome can then dissociate, allowing\nprotein folding within the RER lumen to occur and continuation to the golgi apparatus\nfor processing of the polypeptide.\n2. Iftheproteinisdestinedforstorageforlatersecretionafterstimulationorforcontinuous"
  },
  {
    "chunk_id": 93,
    "source_file": "GeneralBiology.pdf",
    "page": 40,
    "chunk_index_in_page": 2,
    "text": "in folding within the RER lumen to occur and continuation to the golgi apparatus\nfor processing of the polypeptide.\n2. Iftheproteinisdestinedforstorageforlatersecretionafterstimulationorforcontinuous\nsecretion then a protease-enzyme which cuts proteins at the peptide bond-can cut the\nsignal sequence from the growing polypeptide. Continuation to the golgi etc. can then\noccur.\n11 http://en.wikipedia.org/wiki/chromatin\n12 http://en.wikipedia.org/wiki/histone\n13 http://en.wikipedia.org/wiki/nucleosome\n14 http://en.wikipedia.org/wiki/chromatin\n15 http://en.wikipedia.org/wiki/gene%20expression\n16 http://en.wikipedia.org/wiki/replication\n17 http://en.wikipedia.org/wiki/endoplasmic%20reticulum\n18 http://en.wikipedia.org/wiki/organelle\n19 http://en.wikipedia.org/wiki/protein%20synthesis\n20 http://en.wikipedia.org/wiki/lipid%20synthesis\n21 http://en.wikipedia.org/wiki/polypeptide\n32"
  },
  {
    "chunk_id": 94,
    "source_file": "GeneralBiology.pdf",
    "page": 41,
    "chunk_index_in_page": 0,
    "text": "Endoplasmic reticulum\nWhen produced, proteins are then exported to one of several locations. The proteins are\neither modified for extracellular membrane insertion or secretion. Note, this is in contrast\nwithribosomeswhichdonotassociatewiththeRERandproduceproteinswhichwillbecome\ncytosolic enzymes for example.\n8.3.2 Smooth Endoplasmic Reticulum\nSmooth endoplasmic reticulum produces enzyme22s for lipid and carbohydrate biosynthesis\nand detoxification RER\n8.3.3 Sarcoplasmic Reticulum\nThis is a specialised form of endoplasmic reticulum found in some muscle cell types-\nparticularly striated, skeletal muscle. Its main function is different from the other 2 types in\nthat is mainly acts as a storage of calcium. This reticulum has voltage gated channels which\nrespond to signals from 'motor neurones' to open and release calcium into the cytoplasm.\nThis can then bring about the next part in muscle contraction.\nFigure 1 :Image of nucleus23, endoplas-\nmic reticulum and Golgi apparatus.\n1. Nucleus."
  },
  {
    "chunk_id": 95,
    "source_file": "GeneralBiology.pdf",
    "page": 41,
    "chunk_index_in_page": 1,
    "text": "' to open and release calcium into the cytoplasm.\nThis can then bring about the next part in muscle contraction.\nFigure 1 :Image of nucleus23, endoplas-\nmic reticulum and Golgi apparatus.\n1. Nucleus.\n2. Nuclear pore.\n3. Rough endoplasmic reticulum (RER).\n4. Smooth endoplasmic reticulum (SER).\n5. Ribosome on the rough ER.\n6. Proteins that are transported.\n7. Transport vesicle.\n8. Golgi apparatus.\nFigure 4\n9. Cis face of the Golgi apparatus.\n10. Trans face of the Golgi apparatus.\n11. Cisternae of the Golgi apparatus.\n1.\n22 http://en.wikipedia.org/wiki/enzyme\n23 http://en.wikipedia.org/wiki/cell%20nucleus\n33"
  },
  {
    "chunk_id": 96,
    "source_file": "GeneralBiology.pdf",
    "page": 42,
    "chunk_index_in_page": 0,
    "text": "Structure of Eukaryotic cells\n8.4 The Golgi apparatus\nThe golgi apparatus24 is made up of multiple stacks of bilipid membranes.\n• Proteins made on the RER are modified and then sorted\n• Formation of secretory vesicles\n• Formation of lysosomes (intracellular digestion)\nOther membrane-bound cytoplasmic organelles include:\n• Microbodies25 (generic term)\n• Glyoxysome (transforms fat into carbohydrate in plants)\n• Peroxisome26 (uses oxidative metabolism to form hydrogen peroxide and is destroyed by\ncatalase27)\n8.5 Ribosomes\nRibosomes are the site of protein synthesis. Ribosomes themselves are synthesized in the\ncell nucleoli28 and are structured as two subunits, the large and the small. These parts are\ncomposed of RNA and protein.\nProkaryotic and eukaryotic ribosomes are different, the eukaryotic ones being larger and\nmore complicated.\n8.6 DNA-containing organelles\nMitochondria\n• Double membrane\n• Aerobic metabolism, internal membrane\n• DNA, ribosomes\n• Give rise to new mitochondria"
  },
  {
    "chunk_id": 97,
    "source_file": "GeneralBiology.pdf",
    "page": 42,
    "chunk_index_in_page": 1,
    "text": "ukaryotic ones being larger and\nmore complicated.\n8.6 DNA-containing organelles\nMitochondria\n• Double membrane\n• Aerobic metabolism, internal membrane\n• DNA, ribosomes\n• Give rise to new mitochondria\nChloroplast29\n• Double membrane\n• Photosynthesis, internal membrane\n• DNA, ribosomes\n• Give rise to new chloroplasts\nCentriole30s\n24 http://en.wikipedia.org/wiki/Golgi%20apparatus\n25 http://en.wikipedia.org/wiki/Microbody\n26 http://en.wikipedia.org/wiki/Peroxisome\n27 http://en.wikipedia.org/wiki/catalase\n28 http://en.wikipedia.org/wiki/nucleoli\n29 http://en.wikipedia.org/wiki/Chloroplast\n30 http://en.wikipedia.org/wiki/Centriole\n34"
  },
  {
    "chunk_id": 98,
    "source_file": "GeneralBiology.pdf",
    "page": 43,
    "chunk_index_in_page": 0,
    "text": "Cytoskeleton\n• Microtubule organizing centers\n• Animal cells and many protists\n• Pair constitutes the centrosome\n• Give rise to flagellum during spermatogenesis\n• Consist of 9 triplet microtubules\n• Mitosis31, meiosis32\n8.7 Cytoskeleton\nCytoskeleton is a collective term for different filaments of proteins that can give physical\nshape within the cell and are responsible for the 'roads' which organelles can be carried\nalong.\n• Gives the cell shape\n• Anchors other organelles\n• Vital to intracellular transport of large molecules\nThe cytoskeleton is composed of 3 main types of filaments:\n• Actin33 filaments (7 nm)\n• Microtubule34s: (25 nm) polymer of tubulin; 13/ring.\n• Intermediate Filament35s\nBoth actin and microtubules can have associated motor proteins.\n8.7.1 Intermediate Filaments\nThese are rope like filaments, 8-10nm in diameter and tend to give the structural stability to\ncells. Examples inculude Vimentin, neurofilaments and keratin. It is keratin which priniciply"
  },
  {
    "chunk_id": 99,
    "source_file": "GeneralBiology.pdf",
    "page": 43,
    "chunk_index_in_page": 1,
    "text": "Filaments\nThese are rope like filaments, 8-10nm in diameter and tend to give the structural stability to\ncells. Examples inculude Vimentin, neurofilaments and keratin. It is keratin which priniciply\nmakes up hair, nails and horns.\n8.7.2 Actin Filaments\nGrowth\nThese filaments are 2-stranded and composed of dimeric subunits called G-Actin. They\ncontain a GTP molecule in order to bind (polymerise). As GTP is hydrolysed then the\nstructure becomes unstable and depolymerisation occurs. The growth of actin filaments is\nconcentration dependant-that is, the higher the concentration of free G-actin, the greater\nthe polymerisation. The are also polar, having a + and a - end (not related to charge) and\npolymerisation tends to happen faster at the + end.\n31 http://en.wikipedia.org/wiki/mitosis\n32 http://en.wikipedia.org/wiki/meiosis\n33 http://en.wikipedia.org/wiki/Actin\n34 http://en.wikipedia.org/wiki/Microtubule\n35 http://en.wikipedia.org/wiki/Intermediate%20Filament\n35"
  },
  {
    "chunk_id": 100,
    "source_file": "GeneralBiology.pdf",
    "page": 44,
    "chunk_index_in_page": 0,
    "text": "Structure of Eukaryotic cells\nCilia and flagella are threads of microtubules that extend from the exterior of cells and used\nto move single celled organisms as well as move substances away from the surface of the cell.\nmotor proteins-move, wave motion\n36"
  },
  {
    "chunk_id": 101,
    "source_file": "GeneralBiology.pdf",
    "page": 45,
    "chunk_index_in_page": 0,
    "text": "9 Membranes\n9.1 Biological membranes\nFigure 5 Plasma membrane bilayer\n37"
  },
  {
    "chunk_id": 102,
    "source_file": "GeneralBiology.pdf",
    "page": 46,
    "chunk_index_in_page": 0,
    "text": "Membranes\nBiologicalmembranessurroundcellsandservetokeeptheinsidesseparatedfromtheoutsides.\nThey are formed of phospholipid bilayer1s, which by definition are a double layer of fatty\nacid2 molecules (mostly phospholipid3s, lipids containing lots of phosphorus).\nProteins4 serveveryimportantfunctionsincellularmembranes. Theyareactivetransports\nin and out of the cell, acting as gatekeepers. They relay signals in and out of the cell.\nProteins are the site of many enzymatic reactions in the cell, and play a role in\nregulation of cellular processes.\n9.2 Phospholipid\nPhospholipid bilayer\n• basis of biological membranes and cellular organisms\n• contains a charged, hydrophilic (attracted to water) head and two hydrophobic (repelled\nby water) hydrocarbon tails\n• In presence of water, phospholipids form bilayer\n• maximize hydrogen bonds between water\n• creates barrier to passage of materials\n• fluid mosaic model shows horizontal (common) and \"flip-flop\" (rare) movement of\nphospholipids"
  },
  {
    "chunk_id": 103,
    "source_file": "GeneralBiology.pdf",
    "page": 46,
    "chunk_index_in_page": 1,
    "text": "holipids form bilayer\n• maximize hydrogen bonds between water\n• creates barrier to passage of materials\n• fluid mosaic model shows horizontal (common) and \"flip-flop\" (rare) movement of\nphospholipids\n9.3 Fluid mosaic model\n• Current model of membrane\n• Phospholipid bilayer\n• Phospholipids\n• Move freely in lipid layer, but rarely switch layers\n• Different phospholipids in each layer in different organelles\n• Glycolipids\n• Sterols (cholesterol in animals)\n• Transmembrane proteins \"float\" in fluid lipid bilayer\n• also called intrinsic, integral proteins\n• Exterior (extrinsic, peripheral) proteins\n9.4 Membrane proteins\n• Transport channels\n• Enzymes\n• Cell surface receptors\n1 http://en.wikibooks.org/wiki/lipid%20bilayer\n2 http://en.wikibooks.org/wiki/Fatty%20acid\n3 http://en.wikibooks.org/wiki/phospholipid\n4 http://en.wikibooks.org/wiki/Proteins\n38"
  },
  {
    "chunk_id": 104,
    "source_file": "GeneralBiology.pdf",
    "page": 47,
    "chunk_index_in_page": 0,
    "text": "Membrane proteins\n• Cell surface identity markers\n• Cell adhesion proteins\n• Attachments to cytoskeleton\nIntegral membrane proteins\n• Anchoring to membrane\n• Protein has attached phosphatidylinositol (GPI) linkage, anchors protein in outer\nlayer (no picture)\n• Protein has one or more hydrophobic transmembrane domains\n• -helix\n• -sheet\nChannel protein Transport across membranes * Diffusion\n• • From higher concentration to lower concentration\n• Membranes are selectively permeable\n• Ions diffuse through membrane channels\n• Selective\n• Movement determined by diffusion and voltage differences\n• Facilitated diffusion\n• Carrier protein, physically binds transported molecule\n• Osmosis\n• Diffusion of water down concentration gradient\n• In cell: various solutes (amino acids, ions, sugars, etc.)\n• interact with water, e.g., hydration shells\n• Water moves through aquaporin channels into cell\n• Depends upon the concentration of all solutes in solution"
  },
  {
    "chunk_id": 105,
    "source_file": "GeneralBiology.pdf",
    "page": 47,
    "chunk_index_in_page": 1,
    "text": "solutes (amino acids, ions, sugars, etc.)\n• interact with water, e.g., hydration shells\n• Water moves through aquaporin channels into cell\n• Depends upon the concentration of all solutes in solution\n• Hyperosmotic solution: higher concentration of solutes\n• Hypoosmotic solution: lower concentration of solutes\n• Isoosmotic solution: solute concentrations equal\n• Water moves from hypoosmotic solution to hyperosmotic solution\nOsmotic pressure Bulk transport\n• Endocytosis: energy requiring\n• Phagocytosis\n• Solid material, typically food\n• Pinocytosis\n• Primarily liquid\n** Receptor-mediated endocytosis\n• Pits on cell surface coated with clathrin and receptors\n• Bind specific proteins\n• Exocytosis\n• Discharge of materials from vesicle at cell surface\n39"
  },
  {
    "chunk_id": 106,
    "source_file": "GeneralBiology.pdf",
    "page": 48,
    "chunk_index_in_page": 0,
    "text": "Membranes\n9.5 Receptor-mediated endocytosis\nActive transport\n• Energy required (usually ATP)\n• Highly selective\n• Works against concentration gradient\n• Many examples, e.g., Na+/K+ pump\nCotransport (coupled transport)\n• Does not use ATP directly\n• Molecule is transported in connection with another molecule that is moving down a\nconcentration gradient\n• Example: Na+ gradient is established by a Na+ pump, with higher concentration on\noutside of cell. Cotransport channel carries Na+ and another molecule (e.g. glucose)\ninto cell\n• May involve proton (H+) pumps (chemiosmosis - ATP production)\nThis text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the\nCleveland State University.\n40"
  },
  {
    "chunk_id": 107,
    "source_file": "GeneralBiology.pdf",
    "page": 49,
    "chunk_index_in_page": 0,
    "text": "10 Cell-cell interactions\nwith the environment with each other\n10.1 Cell signaling\n• Signaling requires\n• Signal\n• Cell receptor (usually on surface)\n• Signaling is important in:\n• Response to environmental stimuli\n• Sex\n• Development\n• Major area of research in biology today\n10.1.1 Types of signaling\n• Direct contact (e.g., gap junctions between cells)\n• Paracrine: Diffusion of signal molecules in extracellular fluid; highly local\n• Endocrine: Signal (hormone) molecule travels through circulatory system\n• Synaptic: neurotransmitters\nTypes of signal molecules\n• Hormones: chemically diverse\n• Steroid\n• Polypeptide\n• Vitamin/amino acid derived\n• Cell surface proteins/glycoproteins\n• Ca2+, NO\n• Neurotransmitter\n• Several hundred types\n• Some are also hormones e.g. Estrogen, progesterone\nReceptor molecules\n• Intracellular\n• Protein that binds signal molecule in cytoplasm\n41"
  },
  {
    "chunk_id": 108,
    "source_file": "GeneralBiology.pdf",
    "page": 50,
    "chunk_index_in_page": 0,
    "text": "Cell-cell interactions\n• Bound receptor may act as:\n• Gene regulator\n• Enzyme\n• Cell surface\n• Gated ion channels (neurotransmitter receptor)\n• Enzymic receptors\n• G protein-linked receptors\nCell surface protein\n• Tissue identity\n• glycolipids\n• MHC proteins\n• Immune systems\n• distinguish self from not-self\n• Intercellular adhesion\n• permanent contact\n• help form sheets of cells, tissues\n• may permit signaling\nExample: G proteins\n• Transmembrane surface receptor binds signal molecule\n• Conformational change allows binding of G protein on cytoplasmic side\n• G protein binds GTP, becomes activated\n• G protein activates intracellular signal cascade\n• Change in gene expression\n• Secrection\n• Many other possible consequences\n10.2 Communicating junctions\n• Gap junctions\n• animals\n• small molecules and ions may pass\n• Plasmodesmata\n• plants\n• lined with plasma membrane\n• permit passage of water, sugars, etc.\n10.2.1 Gap junctions\nThis text is based on notes very generously donated by Dr."
  },
  {
    "chunk_id": 109,
    "source_file": "GeneralBiology.pdf",
    "page": 50,
    "chunk_index_in_page": 1,
    "text": "olecules and ions may pass\n• Plasmodesmata\n• plants\n• lined with plasma membrane\n• permit passage of water, sugars, etc.\n10.2.1 Gap junctions\nThis text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the\nCleveland State University.\n42"
  },
  {
    "chunk_id": 110,
    "source_file": "GeneralBiology.pdf",
    "page": 51,
    "chunk_index_in_page": 0,
    "text": "11 Energy and Metabolism\n11.1 Energy\n• The capacity to do work.\n• Kinetic energy: energy of motion (ex. jogging).\n• Potential energy: stored energy (ex. a lion that is about to leap on its prey).\n• Many forms of energy: e.g.,\n• Heat\n• Sound\n• Electric current\n• Light\n• All convertible to heat\n• Most energy for biological world is from sun\n• Heat (energy of random molecular motion, thermal energy)\n• Convenient in biology\n• All other energy forms can be converted to heat\n• Thermodynamics: study of thermal energy\n• Heat typically measured in kilocalories\n• Kcal: 1000 calories\n• 1 calorie: amount of heat required to raise the temperature of one gram of water one\ndegree Celsius (°C)\n• Heat plays major role in biological systems\n• Ecological importance\n• Biochemical reactions\n11.2 Oxidation–Reduction\n• Energy flows into biological world from sun\n• Light energy is captured by photosynthesis\n• Light energy raises electrons to higher energy levels"
  },
  {
    "chunk_id": 111,
    "source_file": "GeneralBiology.pdf",
    "page": 51,
    "chunk_index_in_page": 1,
    "text": "nce\n• Biochemical reactions\n11.2 Oxidation–Reduction\n• Energy flows into biological world from sun\n• Light energy is captured by photosynthesis\n• Light energy raises electrons to higher energy levels\n• Stored as potential energy in covalent C-H bonds of sugars\n• Strength of covalent bond is measured by amount of energy required to break it\n• 98.8 kcal/mole of C-H bonds\n• In chemical reaction, energy stored in covalent bonds may transfer to new bonds. When\nthis involves transfer of electrons, it is oxidation–reduction reaction\n• Always take place together\n• Electron lost by atom or molecule through oxidation is gained by another atom or\nmolecule through reduction\n• Potential energy is transferred from one molecule to another (but never 100%)\n43"
  },
  {
    "chunk_id": 112,
    "source_file": "GeneralBiology.pdf",
    "page": 52,
    "chunk_index_in_page": 0,
    "text": "Energy and Metabolism\n• Often called redox reactions\n• Photosynthesis\n• Cellular Respiration\n• Chemiosynthesis\n• Autotrophs\n• Heterotrophs\n+\n11.3 NAD\n• Common electron acceptor/donor in redox reactions\n• Energetic electrons often paired with H+\n11.4 Free energy\n• Energy required to break and subsequently form other chemical bonds\n• Chemical bonds: sharing of electrons, tend to hold atoms of molecule together\n• Heat, by increasing atomic motion, makes it easier to break bonds (entropy)\n• Energy available to do work in a system\n• In cells, G = H - TS\n• G = Gibbs’ free energy\n• H = H (enthalpy) energy in molecule’s chemical bonds\n• TS (T, temperature in °K; S, entropy)\n• Chemical reactions break and make bonds, producing changes in energy\n• Under constant conditions of temperature, pressure and volume, ∆G = ∆H - T∆S\n• ∆G, change in free energy\n• If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction,"
  },
  {
    "chunk_id": 113,
    "source_file": "GeneralBiology.pdf",
    "page": 52,
    "chunk_index_in_page": 1,
    "text": "Under constant conditions of temperature, pressure and volume, ∆G = ∆H - T∆S\n• ∆G, change in free energy\n• If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction,\ndoes not proceed spontaneously; require input of energy (e.g., heat)\n• If negative (–), H is lower, S is higher. Product has less free energy; exergonic;\nspontaneous\n===Activation energy = ==\n• Reactions with –∆G often require activation energy\n• e.g., burning of glucose\n• Must break existing bonds to get reaction started\n• Catalysts lower activation energy\n11.5 Enzymes\n• Biological catalysts\n• Protein\n• RNA (ribozyme)\n• Stabilizes temporary association between reactants (substrates) to facilitate reaction\n• Correct orientation\n• Stressing bonds of substrate\n44"
  },
  {
    "chunk_id": 114,
    "source_file": "GeneralBiology.pdf",
    "page": 53,
    "chunk_index_in_page": 0,
    "text": "Enzymes\n• Lower activation energy\n• Not consumed (destroyed) in reaction\n11.5.1 Carbonic anhydrase\n• Important enzyme of red blood cells\n• CO + H O → H CO -> HCO + H+\n2 2 2 3 3\n• Carbonic anhydrase catalyzes 1st reaction\n• Converts water to hydroxyl\n• Orients the hydroxyl and CO\n2\n11.5.2 Enzyme mechanism\n• One or more active sites which bind substrates (reactants)\n• Highly specific\n• Binding may alter enzyme conformation, inducing better fit\n11.5.3 Factors affecting enzyme activity\n• Substrate concentration\n• Product concentration\n• Cofactor concentration\n• Temperature\n• pH\n• Inhibitors\n• Competitive: bind to active site\n• Noncompetitive: bind to 2nd site, called allosteric site; changes enzyme conformation\n• Activators\n• Bind to allosteric sites, increase enzyme activity\nCofactors\n• Required by some enzymes\n• Positively charged metal ions\n• e.g., ions of Zn1, Mo, Mg, Mn\n• Draw electrons away from substrate (stress chemical bonds)\n• Non-protein organic molecules (coenzymes)"
  },
  {
    "chunk_id": 115,
    "source_file": "GeneralBiology.pdf",
    "page": 53,
    "chunk_index_in_page": 1,
    "text": "ors\n• Required by some enzymes\n• Positively charged metal ions\n• e.g., ions of Zn1, Mo, Mg, Mn\n• Draw electrons away from substrate (stress chemical bonds)\n• Non-protein organic molecules (coenzymes)\n• E.g., NAD+, NADP+, etc.\n• Major role in oxidation/reduction reactions by donating or accepting electrons\n1 http://en.wikibooks.org/wiki/Zinc\n45"
  },
  {
    "chunk_id": 116,
    "source_file": "GeneralBiology.pdf",
    "page": 54,
    "chunk_index_in_page": 0,
    "text": "Energy and Metabolism\n11.6 ATP\n• Adenosine triphosphate\n• Major energy currency of cells, power endergonic reactions\n• Stores energy in phosphate bonds\n• Highly negative charges, repel each other\n• Makes these covalent bonds unstable\n• Low activation energy\n• When bonds break, energy is transferred\n• ATP → ADP + Pi + 7.3 kcal/mole\n11.7 Biochemical pathways\n• Metabolism: sum of chemical reactions in cell/organism\n• Many anabolic and catabolic reactions occur in sequences (biochemical pathways)\n• Often highly regulated\nEvolution of biochemical pathways\n• Protobionts or 1st cells likely used energy rich substrates from environment\n• Upon depletion of a substrate, selection would favor catalyst which converts another\nmolecule into the depleted molecule\n• By iteration, pathway evolved backward\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n46"
  },
  {
    "chunk_id": 117,
    "source_file": "GeneralBiology.pdf",
    "page": 55,
    "chunk_index_in_page": 0,
    "text": "12 Respiration: harvesting of energy\nGlucose + O → CO + H O + ATP\n2 2 2\n12.1 Energy\n• Energy is primarily in C-H bonds (C-O too)\n• Chemical energy drives metabolism\n• Autotrophs: harvest energy through photosynthesis or related process (plants, algae,\nsome bacteria)\n• Heterotrophs: live on energy produced by autotrophs (most bacteria and protists,\nfungi, animals)\n• Digestion: enzymatic breakdown of polymers into monomers\n• Catabolism: enzymatic harvesting of energy\n• Respiration: harvesting of high energy electrons from glucose\n12.2 Respiration\n• Transfer of energy from high energy electrons of glucose to ATP\n• Energy depleted electron (with associated H+) is donated to acceptor molecule\n• Aerobic respiration: oxygen accepts electrons, forms water\n• Anaerobic respiration: inorganic molecule accepts hydrogen/electron\n• Fermentation: organic molecule accepts hydrogen/electron\n12.3 Respiration of glucose\n• C H O + 6 O → 6 CO + 6 H O + energy\n6 12 6 2 2 2"
  },
  {
    "chunk_id": 118,
    "source_file": "GeneralBiology.pdf",
    "page": 55,
    "chunk_index_in_page": 1,
    "text": "bic respiration: inorganic molecule accepts hydrogen/electron\n• Fermentation: organic molecule accepts hydrogen/electron\n12.3 Respiration of glucose\n• C H O + 6 O → 6 CO + 6 H O + energy\n6 12 6 2 2 2\n• ∆G = -720 kcal/mole under cellular conditions\n• Largely from the 6 C-H bonds\n• Same energy whether burned or catabolized\n• In cells, some energy produces heat, most is transferred to ATP\n12.4 Alternative anaerobic respiration\n• Methanogens (Archaebacteria).\n• CO is electron acceptor, forming CH\n2 4\n47"
  },
  {
    "chunk_id": 119,
    "source_file": "GeneralBiology.pdf",
    "page": 56,
    "chunk_index_in_page": 0,
    "text": "Respiration: harvesting of energy\n• Sulfur bacteria\n• SO reduced to H S\n4 2\n• Formation of H S set stage for evolution of photosynthesis (H S as electron donor\n2 2\nbefore H O)\n2\n• About 2.7 by, based on ratio of 32S/34S, where only biological processes produce 32S\nenrichment\n12.5 Glycolysis overview\nGlycolysis accounting\n• Oxidation\n• Two electrons (one proton) are transferred from each G3P to NAD+ forming NADH\n2NADH\n• Substrate level phosphorylation\n• G3P to pyruvate forms 2 ATP molecules\n4 ATP (from 2 G3P)\n–2 ATP (priming)\n2 ATP (net gain)\nSummary: The net input of glycolysis is 2 ATP molecules which are used to split one glucose\nmolecule. The net yield of this step is 2 ATP and 2 pyruvate.\n+\n12.6 Regeneration of NAD\n• Reduction of NAD+ to NADH can deplete NAD+ supply; it must be regenerated\n• Two pathways, coupled to fate of pyruvate\n• With oxygen: enter electron transport chain, forming water (and ATP)\n• Without oxygen: fermentation\n• lactate\n• ethanol\n12.7 Alcohol fermentation"
  },
  {
    "chunk_id": 120,
    "source_file": "GeneralBiology.pdf",
    "page": 56,
    "chunk_index_in_page": 1,
    "text": "nerated\n• Two pathways, coupled to fate of pyruvate\n• With oxygen: enter electron transport chain, forming water (and ATP)\n• Without oxygen: fermentation\n• lactate\n• ethanol\n12.7 Alcohol fermentation\n12.8 Lactate formation\nEither lactic acid1 or alcohol can be formed as a result of anaerobic respiration in cells.\n1 http://en.wikipedia.org/wiki/Lactate\n48"
  },
  {
    "chunk_id": 121,
    "source_file": "GeneralBiology.pdf",
    "page": 57,
    "chunk_index_in_page": 0,
    "text": "Krebs cycle: overview\n12.9 Krebs cycle: overview\n• Matrix of mitochondrion\n• Priming steps\n• Joining of acetyl-CoA to oxaloacetate\n• Isomerization reactions\n• Energy extraction steps in Krebs cycle\n• Per glucose\n• 6 NADH\n• 2 FADH\n2\n• 2 ATP (from GTP)\n• 4 CO\n2\n12.10 ATP production\n• Chemiosmosis (Mitchell)\n• H+ (from NADH and FADH ) is pumped against a gradient into the intermembranal\n2\nspace of the mitochondrion (creates voltage potential)\n• Diffusion back into matrix through ATP synthase channels drives synthesis of ATP (ADP\n+ Pi → ATP)\n• ATP exits mitochondrion by facilitated transport\n12.11 Evolution of aerobic respiration\n• Preceded by evolution of photosynthesis (O2 needed; also, prior evolution of electron\ntransport and chemiosmosis)\n• High efficiency of ATP production compared to glycolysis\n• Fostered evolution of heterotrophs\n• Fostered evolution of mitochondria by endosymbiosis in eukaryotes\n49"
  },
  {
    "chunk_id": 122,
    "source_file": "GeneralBiology.pdf",
    "page": 59,
    "chunk_index_in_page": 0,
    "text": "13 Photosynthesis\n6 CO + 6 H O → C H O + 6 O\n2 2 6 12 6 2\n• One of most important reactions in history of life:\n• source of atmospheric O\n2\n• ultimately led to aerobic respiration and eukaryotes\n• Responsible for bulk of glucose production\n• Early experiments showed that mass of plant must be derived from substances in the air,\nnot the soil\n• Experiments with isotopes showed that liberated oxygen comes from water\n• Experiments also showed that light is essential but that some reactions (e.g., reduction of\nCO ) continue in the dark\n2\n• Plants do two big, important things during photosynthesis: gain energy (absorb light)\nand build sugar (glucose).\n• Photosynthesis can be divided into two series of chemical reactions: the light (light-\ndependent) reactions and the dark (light-independent) reactions. In light reactions, light\nis absorbed; in dark reactions, sugar is built.\n• Occurs when plants, algae, and autotrophic bacteria absorb light energy and build glucose.\n13.1 Light Reactions"
  },
  {
    "chunk_id": 123,
    "source_file": "GeneralBiology.pdf",
    "page": 59,
    "chunk_index_in_page": 1,
    "text": "reactions. In light reactions, light\nis absorbed; in dark reactions, sugar is built.\n• Occurs when plants, algae, and autotrophic bacteria absorb light energy and build glucose.\n13.1 Light Reactions\n• Part of the electromagnetic spectrum\n• Consists of units of energy called photons\n• Photons at UV end of spectrum have more energy than those at the red end\n• Occur on the surface of thylakoid disks\n• Chlorophyll and other plant pigments differentially absorb photons\n• Chlorophyll a: light to chemical energy\n• Chlorophyll b: accessory chlorophyll\n• Chlorophylls absorb primarily blue and red (green reflected back, hence the green\ncolor of plants)\n13.1.1 Accessory pigments\n• Chlorophyll is a major light gathering pigment\n• Absorbs light with considerable efficiency (i.e., retaining energy)\n• Accessory pigments\n• Chlorophyll b\n• Carotenoinds\n• capture light of wavelengths not captured by chlorophylls\n51"
  },
  {
    "chunk_id": 124,
    "source_file": "GeneralBiology.pdf",
    "page": 60,
    "chunk_index_in_page": 0,
    "text": "Photosynthesis\n• Confer other colors to plant leaves (autumn colors too)\nPhotosynthetic steps\n• Primary photoevent: light photon captured by photosystem and energy transferred to\nelectron donated by water\n• Electron transport: excited electron is shuttled along imbedded series of electron carriers\nto proton pump and electron is transferred to acceptor\n• Chemiosmosis: transport of protons back into chloroplast drives synthesis of ATP\n13.1.2 The Even More Detailed Light Reactions\nWhat the Light Reactions Do:\nThe light reactions of photosynthesis occur in chloroplasts in and on the thylakoid disks.\nDuring the light reactions, light energy charges up ATP molecules. More specifically, light\nturns the chloroplast into an acid battery, and this battery charges up ATP.\nHow the \"Chloroplast-Battery\" Charges ATP:\nThe stroma is the fluid inside of the chloroplasts, and it carries a negative charge. This\nmeans that it contains about a \"gazillion\" extra electrons. The solvent of stroma is water."
  },
  {
    "chunk_id": 125,
    "source_file": "GeneralBiology.pdf",
    "page": 60,
    "chunk_index_in_page": 1,
    "text": "ry\" Charges ATP:\nThe stroma is the fluid inside of the chloroplasts, and it carries a negative charge. This\nmeans that it contains about a \"gazillion\" extra electrons. The solvent of stroma is water.\nThe fluid inside the thylakoid disks is positively charged because it contains a lot of hydrogen\n(H+) ions. The pH here is low, making the fluid very acidic. The solvent of thylakoid disk\nfluid is water.\nA chloroplast acts like a battery, because it has separated a strong positive charge and a\nstrong negative charge in two different compartments. Energy is released when H+ ions\n(free protons) flow from the inside of a thylakoid disk to the stroma. This is electrical energy,\nsince it is a flow of charged particles.\nThe protons pass through special channels (made of protein) in the thylakoid membrane;\nthis reaction is 'exothermic.' The energy that is given off is used to fuel this reaction (Pi is\nthe phosphate ion):\nADP + Pi --> ATP"
  },
  {
    "chunk_id": 126,
    "source_file": "GeneralBiology.pdf",
    "page": 60,
    "chunk_index_in_page": 2,
    "text": "ugh special channels (made of protein) in the thylakoid membrane;\nthis reaction is 'exothermic.' The energy that is given off is used to fuel this reaction (Pi is\nthe phosphate ion):\nADP + Pi --> ATP\nThe proton can go to the negative stroma, but only if it uses its energy to charge up ATP.\nSince one reaction wants to go, and the other one doesn't, and since the first reaction releases\nenergy and the second one absorbs energy, the two reactions are known to be 'coupled'\ntogether so that the first fuels the second. Of course, a special enzyme must be involved for\nthis to happen.\nChlorophyll Molecules on a Thylakoid Disk:\nHundreds of chlorophyll molecules cover the surface of a thylakoid disk, making the disk\ngreen. The nonpolar \"tails\" of the chlorophyll molecule are embedded in the membrane of\nthe thylakoid.\n52"
  },
  {
    "chunk_id": 127,
    "source_file": "GeneralBiology.pdf",
    "page": 61,
    "chunk_index_in_page": 0,
    "text": "“Dark” reactions\n13.2 “Dark” reactions\n• ATP drives endergonic reactions\n• NADPH provides hydrogens for reduction of CO to carbohydrate (C-H bonds)\n2\n• Occur in the stroma\n• First step in carbon fixation\n13.2.1 The Detailed Dark Reactions\nWhat the Dark Reactions Do:\nThe dark reactions build sugar from carbon dioxide gas (CO2), water (H2O), and energy\nfrom ATP molecules that were charged up during the light reactions. The dark reactions\noccur in the stroma of a chloroplast. Dark reactions usually occur in the light, but they\ndon't have to. They'll occur in the dark until the chloroplast's supply of ATP runs out\n(usually about 30 seconds).\nThe Calvin Cycle:\nThe Calvin Cycle is the fancy name for the metabolic pathway that builds sugar. This\nmeans that it involves a whole lot of chemical reactions, and it uses a lot of different enzymes\nto catalyze the reactions.\nCarbon dioxide gas is stable, therefore the bonds that hold the carbon and oxygen atoms\nare strong."
  },
  {
    "chunk_id": 128,
    "source_file": "GeneralBiology.pdf",
    "page": 61,
    "chunk_index_in_page": 1,
    "text": "a whole lot of chemical reactions, and it uses a lot of different enzymes\nto catalyze the reactions.\nCarbon dioxide gas is stable, therefore the bonds that hold the carbon and oxygen atoms\nare strong. Therefore it takes a lot of energy to break the bonds and separate the carbon\natoms from the oxygen atoms. The energy needed to do this comes from ATP molecules.\nWhen inorganic carbon (like from CO2) is being added to an organic molecule (such as\nsugar), this is called carbon fixation.\nIt takes 2 complete turns of the Calvin Cycle to make a glucose molecule.\nSome portions of this text is based on notes very generously donated by Paul Doerder, Ph.D.,\nof the Cleveland State University. The detailed portions are not provided by Dr. Doerder.\nHow cells divide\n13.3 Prokaryote cell division\n• Binary fission\n• Doubling of cell contents, including DNA\n• Fission to divide contents\n• Segregation of replicated genomes by growth of membrane between attachment points"
  },
  {
    "chunk_id": 129,
    "source_file": "GeneralBiology.pdf",
    "page": 61,
    "chunk_index_in_page": 2,
    "text": "3 Prokaryote cell division\n• Binary fission\n• Doubling of cell contents, including DNA\n• Fission to divide contents\n• Segregation of replicated genomes by growth of membrane between attachment points\n• Partitioning of cytoplasmic components\n• Escherichia coli\n• Capable of cell division every 20 minutes under optimal conditions (DNA in continuous\nstate of replication)\n• Model organism of bacterial cell division\n53"
  },
  {
    "chunk_id": 130,
    "source_file": "GeneralBiology.pdf",
    "page": 62,
    "chunk_index_in_page": 0,
    "text": "Photosynthesis\n13.4 Bacterial DNA replication\n• Replication follows rules of base pairing, with each polynucleotide chain serving as\ntemplate for synthesis of its complement.\n• Genetic evidence showed that the bacterial chromosome is circular long before there was\ncorroborating physical evidence.\nEukaryotic chromosomes\n• Discovered by Walther Fleming in 1882 in dividing cells of salamander larvae, following\nimprovements in microscopes and staining technology\n• He called division mitosis (mitos = “thread”)\n• Chromosome number is constant in a species\n• Ranges from 2 to >500 (46 in human somatic cells)\n• Homologous pairs, one contributed by each parent\n• Change in number is cause and consequence of speciation\n• Chromosome constancy and their precise division in mitosis and meiosis led biologists to\npostulate that they were carriers of hereditary information\n13.5 Chromosome number\n• 1N = number of chromosomes in gamete\n• 1N = haploid chromosome number"
  },
  {
    "chunk_id": 131,
    "source_file": "GeneralBiology.pdf",
    "page": 62,
    "chunk_index_in_page": 1,
    "text": "ion in mitosis and meiosis led biologists to\npostulate that they were carriers of hereditary information\n13.5 Chromosome number\n• 1N = number of chromosomes in gamete\n• 1N = haploid chromosome number\n• 2N = number of chromosomes in somatic cells (cells that are not egg or sperm)\n• 2N = diploid\n• Deviations from N or 2N are usually lethal in animals\nChromosome numbers\n13.6 Eukaryotic chromosomes\n• Consist of chromatin\n• DNA and associated proteins, mainly histones\n• Nucleosomal organization\n• Euchromatin: unwound chromatin, in basic nucleosomal configuration; genes available\nfor expression\n• Heterochromatin: highly condensed except during replication\n• Karyotype: array of chromosomes an individual possesses\n• Clinical importance (Down syndrome; cancer)\n• Evolutionary importance (speciation)\n54"
  },
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    "page": 63,
    "chunk_index_in_page": 0,
    "text": "Chromosome organization\n13.7 Chromosome organization\n13.8 Human karyotype stained by chromosome painting\n13.9 Chromosomes\n• Homologous pairs\n• Inherited one from each parent\n• Identical in length and position of centromere\n• Contain identical or similar genes\n• Homologous pair = homologs\n• Morphology\n• After replication, consist of two sister chromatids attached to a centromere\n13.10 Human chromosomes\n• Diploid number = 2n = 46 = 23 pairs of homologs\n• Haploid number = 23 (gametes)\n• Each replicated chromosome contains 2 sister chromatids = 92 chromatids\nCell cycle\n• Growth and division cycle of cells\n• Precisely controlled by biochemical and gene activity, except in cancer\n• Phases\n• G1: primary growth phase\n• S: DNA replication; chromosome replication\n• G2: second growth phase; preparation for mitosis\n• M: mitosis; nuclear division\n• C: cytoplasmic division\n13.11 Mitotic cell cycle\n• Cells exiting the cell cycle are said to be in G0"
  },
  {
    "chunk_id": 133,
    "source_file": "GeneralBiology.pdf",
    "page": 63,
    "chunk_index_in_page": 1,
    "text": "me replication\n• G2: second growth phase; preparation for mitosis\n• M: mitosis; nuclear division\n• C: cytoplasmic division\n13.11 Mitotic cell cycle\n• Cells exiting the cell cycle are said to be in G0\n• Cell cycle time varies with stages of life cycle and development, with G1 the most variable\n• DNA replication occurs during S phase of the cell cycle following G1.\n- at this point the chromosomes are composed of two sister\nchromotids connected by a common centromere.\n55"
  },
  {
    "chunk_id": 134,
    "source_file": "GeneralBiology.pdf",
    "page": 64,
    "chunk_index_in_page": 0,
    "text": "Photosynthesis\n13.12 Replicated human chromosomes\n13.13 Mitosis\n• Nuclear division\n• equational division of replicated chromosomes\n• chromatids move to opposite poles\n• Continuous process\n• prophase\n• metaphase\n• anaphase\n• telophase\n• Driven by motors and microtubules\n• No change in chromosome number\n• N → N by mitosis\n• 2N → 2N by mitosis\n• May be accompanied by cytokinesis\nKinetochore Microtubules attach to kinetochores. Metaphase\n• Momentary alignment of chromosomes in center of cell\nAnaphase\n13.14 Plant mitosis\n• Similar to animal mitosis\n• New cell wall formed between cells from membrane partition\nCell cycle control\n• Cell cycle events are regulated by protein complexes and checkpoints\n• Discovered by microinjection of proteins in to eggs, by mutational analysis and by\ntechniques of molecular biology\nMolecular control of cell cycle: Cdk and cyclin\n• Cyclin dependent protein kinase (Cdk)\n• Phosphorylate serine/threonine of target regulatory proteins"
  },
  {
    "chunk_id": 135,
    "source_file": "GeneralBiology.pdf",
    "page": 64,
    "chunk_index_in_page": 1,
    "text": "analysis and by\ntechniques of molecular biology\nMolecular control of cell cycle: Cdk and cyclin\n• Cyclin dependent protein kinase (Cdk)\n• Phosphorylate serine/threonine of target regulatory proteins\n• Function only when bound to cyclin\n• Cyclin: short-lived proteins that bind to cdks\n13.15 Controlling the cell cycle\n• External signals initiate cell division in multicellular organisms\n• Growth factors: extracellular regulatory signals\n• Usually soluble; bind to cell surface receptor\n56"
  },
  {
    "chunk_id": 136,
    "source_file": "GeneralBiology.pdf",
    "page": 65,
    "chunk_index_in_page": 0,
    "text": "Cancer\n• Sometimes membrane bound, requiring cell-cell contact with receptor\n• E.g., upon wound, platelets release PDGF which stimulates fibroblasts to enter cell\ncycle (exit G0), to heal wound\n13.16 Cancer\n• Unregulated cell proliferation\n• Cancer cells have numerous abnormalities\n• >46 chromosomes\n• Mutations in proto-oncogenes\n• Encode proteins stimulating the cell cycle\n• May be regulated by phosphorylation\n• Often over expressed in cancer cells\n• Mutations in tumor-suppressor genes\n• Encode proteins inhibiting the cell cycle\n• Often bind to products of proto-oncogenes\n• May be regulated by phosphorylation\n13.17 Mutations and cancer\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n57"
  },
  {
    "chunk_id": 137,
    "source_file": "GeneralBiology.pdf",
    "page": 67,
    "chunk_index_in_page": 0,
    "text": "14 Sexual reproduction\n14.1 Sexual\n• Exclusively eukaryotes\n• Fusion of two haploid genomes\n• Fertilization (= syngamy)\n• Forms new individuals in multicellular organisms as result of fusion of egg and sperm\n• Plants\n• Animals\n• Meiosis yields haploid genomes at some point in life cycle\n14.2 Sexual life cycle\nTypical animal life cycle\n• Meiosis occurs in germ line cells in gonads producing haploid gametes\n• All other cells are somatic cells\n• Alternation of generations\n• Sexual intercourse\n14.3 Meiosis\n• Gives rise to genetic variation\n• Reduction division: 2n to n\n• Preceded by one round of DNA (chromosome) replication\n• Two rounds of nuclear (& usually cell) division\n• Meiosis I\n• Synapsis of homologs\n• Segregation of homologs\n• Reduction division, 2n to n\n• Meiosis II\n• No chromosome replication\n• Segregation of sister chromatids\n• Formation of 4 haploid (n) cells\n• Two nuclear divisions, usually 2 cell divisions, only one round of replication\n• Meiosis I"
  },
  {
    "chunk_id": 138,
    "source_file": "GeneralBiology.pdf",
    "page": 67,
    "chunk_index_in_page": 1,
    "text": "iosis II\n• No chromosome replication\n• Segregation of sister chromatids\n• Formation of 4 haploid (n) cells\n• Two nuclear divisions, usually 2 cell divisions, only one round of replication\n• Meiosis I\n• Prophase: synapsis and crossing over\n• Metaphase\n59"
  },
  {
    "chunk_id": 139,
    "source_file": "GeneralBiology.pdf",
    "page": 68,
    "chunk_index_in_page": 0,
    "text": "Sexual reproduction\n• Anaphase: chromosome segregation\n• Telophase\n• Meiosis II (mitosis-like)\n• Prophase\n• Metaphase\n• Anaphase: sister chromosome segregation\n• Telophase\n14.4 Prophase I: synapsis\n• Complete alignment of replicated homologs\n• Synapsis occurs throughout the entire length of a pair of homologs\n• Key to chromosome segregation\n• Synapsis, crossing over\n• Subdivided into 5 continuous stages\n14.5 Crossing over\n• Reciprocal, physical exchange between nonsister chromatids\n• Type of recombination; mixes maternal and paternal genes\n• Visual evidence: chiasmata\n14.6 Microtubules and anaphase I\n• During prophase microtubules attach to kinetochores on one side of centromere\n• The metaphase checkpoint insures proper attachment\n• A phosphorylation event initiates motor activity and anaphase\n14.7 Meiosis II\n• Cytologically similar to mitosis\n• No preceding DNA replication\n• Chromatids segregate and move to opposite poles as chromosomes\n• 4 haploid cells produced"
  },
  {
    "chunk_id": 140,
    "source_file": "GeneralBiology.pdf",
    "page": 68,
    "chunk_index_in_page": 1,
    "text": "tor activity and anaphase\n14.7 Meiosis II\n• Cytologically similar to mitosis\n• No preceding DNA replication\n• Chromatids segregate and move to opposite poles as chromosomes\n• 4 haploid cells produced\n• In animals, these cells differentiate into gametes\n• In plants and many other organisms, these cells divide by mitosis, followed some time\nlater by gamete formation\n14.8 Evolution of sex\n• Asexual reproduction: all offspring genetically identical to parent\n60"
  },
  {
    "chunk_id": 141,
    "source_file": "GeneralBiology.pdf",
    "page": 69,
    "chunk_index_in_page": 0,
    "text": "Consequences of sex\n• Sex: recombination destroys advantageous combinations\n• So why sex?\n• Many hypotheses\n• Effect repair of genetic damage?\n• Much pachytene repair as well as gene conversion\n• Some protists form diploid cells in response to stress\n• Recombination breaks up combinations of genes favoring parasites, thus reducing\nparasitism?\n14.9 Consequences of sex\n• Recombination: generates genetic diversity\n• Crossing over\n• Independent assortment\n• Random fertilization\n• Qualities of gamete usually do NOT reflect qualities of genes enclosed in gamete\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n61"
  },
  {
    "chunk_id": 142,
    "source_file": "GeneralBiology.pdf",
    "page": 71,
    "chunk_index_in_page": 0,
    "text": "15 Genetics\n63"
  },
  {
    "chunk_id": 143,
    "source_file": "GeneralBiology.pdf",
    "page": 73,
    "chunk_index_in_page": 0,
    "text": "16 Gregor Mendel and biological\ninheritance\nCharles Darwin1, for all he contributed to the science of biology, never knew about the\nmechanism by which living things inherit traits from previous generations, or how new traits\narise.\nAs any schoolchild can tell you, this mechanism of interitance has since been found to be\nDNA2, or deoxyribonucleic acid. DNA allows for stable inheritance of traits: the code in\neach strand of DNA is replicated precisely through the pairing of basic units along each\nstrand. The error rate in this replication is amazingly low; not even one base pair in a\nmillion matches out of sequence.\nHowever, when even one base pair is added to a new strain of DNA in an order differently\nthanintheparentchain,itcanbethebasisofamutation. ThesechangesinDNAsequences\nare the microscopic origin of changes in traits of all studied living things. Even the smallest\ndifference in a strand of DNA can result in a change in traits that can cost the life of the\norganism."
  },
  {
    "chunk_id": 144,
    "source_file": "GeneralBiology.pdf",
    "page": 73,
    "chunk_index_in_page": 1,
    "text": "s\nare the microscopic origin of changes in traits of all studied living things. Even the smallest\ndifference in a strand of DNA can result in a change in traits that can cost the life of the\norganism. Mutations can produce proteins with a new or altered function. In humans, the\nexample of Sickle cell anemia3 is commonly given as its origin is a difference of only one\nbase pair in a section of DNA that encodes red blood cells.\nIndividual sequences of DNA that encode for specific proteins are called genes and are the\nunits of heredity. Each one has a set nucleotide4, and together all of the genes (and some\nsequence of DNA that apparently do not code for any biologically important functions)\ntogether make up the entire chromosome5\n16.1 Mendel\n• Discovered principle of genetic segregation via numerous experiments utilizing pea plants\n• Inferred the existence of genes through segregation of phenotypes\n• Used quantitative methods: counted; ratios\n• Work is model of scientific method"
  },
  {
    "chunk_id": 145,
    "source_file": "GeneralBiology.pdf",
    "page": 73,
    "chunk_index_in_page": 2,
    "text": "ion via numerous experiments utilizing pea plants\n• Inferred the existence of genes through segregation of phenotypes\n• Used quantitative methods: counted; ratios\n• Work is model of scientific method\n• In particular, observed the F2 progeny, which lead to the discovery of dominant and\nrecessive traits\n• Published work in 1866, went unnoticed\n• In 1900 his scientific paper was “rediscovered”\n1 http://en.wikibooks.org/wiki/Charles%20Darwin\n2 http://en.wikipedia.org/wiki/DNA\n3 http://en.wikipedia.org/wiki/Sickle%20cell%20anaemia\n4 http://en.wikipedia.org/wiki/nucleotide\n5 http://en.wikipedia.org/wiki/chromosome\n65"
  },
  {
    "chunk_id": 146,
    "source_file": "GeneralBiology.pdf",
    "page": 74,
    "chunk_index_in_page": 0,
    "text": "Gregor Mendel and biological inheritance\n• Mendel is acknowledged as founder of Genetics\n• still used alphabet letters to designate genes\n• still refer to dominant and recessive genes\n• still refer to segregation of alleles in meiosis\n• principle of segregation applies to all sexually reproducing organisms; Mendel’s results\nwere immediately applied to humans in 1900\n16.2 Mendel’s experiments\n• 1856, began experiments with the garden pea, Pisum sativum\n• 1865, presented results to the Bruno natural history society, which he helped found\n• 1866, published his results in proceedings of the society\n• Naegeli encouraged Mendel to reproduce results in another species, which failed because\nthe species did not undergo true fertilization\n• discrete traits in Pisum sativum\n• pure-breeding lines\n• dominant/recessive alleles\n• alleles are two alternate versions of a gene\n• gametes contain hybridized chromosomes that are formed during meiosis\n• homozygous has two of the same allele"
  },
  {
    "chunk_id": 147,
    "source_file": "GeneralBiology.pdf",
    "page": 74,
    "chunk_index_in_page": 1,
    "text": "eding lines\n• dominant/recessive alleles\n• alleles are two alternate versions of a gene\n• gametes contain hybridized chromosomes that are formed during meiosis\n• homozygous has two of the same allele\n• heterozygous has two different alleles\n• reciprocal F1 crosses (all exhibiting dominant phenotypes); F2; F3\n• counted offspring, noted ratios\n• inferred genotypes from phenotypes\n• tested hypotheses with testcrosses\n• attempted to repeat with another species\n16.3 Mendel’s seven pairs of traits\n1. Seed form (round or wrinkled)\n2. Cotyledon color (green or yellow)\n3. Seed coat color (white or colored)\n4. Pod form (inflated or constricted)\n5. Pod color (green or yellow)\n6. Flower position (axial or terminal)\n7. Plant heights (tall or short)\n16.4 Locus\n• The location of a specific gene within a chromosome\n66"
  },
  {
    "chunk_id": 148,
    "source_file": "GeneralBiology.pdf",
    "page": 75,
    "chunk_index_in_page": 0,
    "text": "Modern Y chromosome\n16.5 Modern Y chromosome\nY-chromosome is the most evolved chromosome. Generally it is thought that if Y- chro-\nmosome is present in an individual then he will be male. But if mutation occurs at sex\ndetermining region or zinc factor then it will not code for testis determining factor, and\nresults in normal female. This type of female's frequency is 1/250000.\n16.6 Chromosome phenomena\n• X-chromosome inactivation\n• Barr bodies\n• Nondisjunction: failure of chromosome segregation at meiosis or mitosis\n• Results in 2N ± 1 chromosome number\n• Trisomy 2N + 1\n• Usually lethal. Trisomy 21 (Down) exception\n• Monosomy 2N ** 1\n• Lethal except XO\n• Usually maternal origin in humans\n16.7 X-chromosome inactivation\nIn females, one X-chromosone is randomly switched off forming a Barr body.\n16.8 Barr body\nDense region in the nucleus formed by the inactive X-chromosome.\n16.9 Human genetic disorders\nDown's Syndrome(Mongolism)"
  },
  {
    "chunk_id": 149,
    "source_file": "GeneralBiology.pdf",
    "page": 75,
    "chunk_index_in_page": 1,
    "text": "one X-chromosone is randomly switched off forming a Barr body.\n16.8 Barr body\nDense region in the nucleus formed by the inactive X-chromosome.\n16.9 Human genetic disorders\nDown's Syndrome(Mongolism)\nDown's Syndrome is usually produced by the nondisjunction of chromosome 21 during\noogenesis and sometimes during spermatogenesis. The individual suffering from this type of\nsyndrome has 47 chromosomes instead of the normal 46. The extra chromosome is not a sex\nchromosome but an autosome.\nMost cases of mongolism were found to occur in children born by women in their forties.\nThe affected children, called mongoloids, show mental retardation and have a shorter life\nexpectancy. Their most prominent feature is the Mongolian folds in their eyes; hence, the\nterm mongolism.\nKlinefelter's Syndrome\n67"
  },
  {
    "chunk_id": 150,
    "source_file": "GeneralBiology.pdf",
    "page": 76,
    "chunk_index_in_page": 0,
    "text": "Gregor Mendel and biological inheritance\nWhen an XY-bearing sperm unites with an X-bearing egg, the resulting condition is called\nKlinefelter's Syndrome, or sexually undeveloped male. Individuals having the syndrome\nshow the following characteristics:\n• testes are small\n• sperms are never produced\n• breasts are enlarged\n• body hair is sparse\n• individuals are mentally defective\nThe same abnormal meiotic division may occur in females. They produce eggs with XX or\nno sex chromosomes. Such egg, when fertilized by a Y-bearing sperm, will not develop (YO).\nThis is because YO is lethal--it wil cause death to the offspring.\n68"
  },
  {
    "chunk_id": 151,
    "source_file": "GeneralBiology.pdf",
    "page": 77,
    "chunk_index_in_page": 0,
    "text": "17 DNA: The Genetic Material\n17.1 DNA\nDNA stands for Deoxyribose Nucleic Acid. That is, a nucleic acid with two sugars. DNA is\nthe hereditary material of cells and is considered the blueprint of life. DNA is found in all\nkingdoms of life. Even most viruses have DNA. A molecule of DNA is chemically stable (it\ndoes not have a 2-prime alcohol group.)\nWhen someone says DNA, they may be referring to one's genetic material on multiple levels:\nThey may be speaking about a single deoxyribose nucleic acid molecule, a section of a double\nhelix, a section of a chromosome, or one's entire hereditary composition.\n• antiparallel\n• Double helix\n• Semiconservative replication\n• Sequence of nucleotides encodes functional RNA or polypeptide\n17.2 Historical perspective\n• Mitosis and meiosis\n• Regular distribution of chromosomes suggested that they contain hereditary informa-\ntion\n• Bridges/Morgan,usingDrosophilamelanogastershowedthatgenesareonchromosomes\n(1910s)"
  },
  {
    "chunk_id": 152,
    "source_file": "GeneralBiology.pdf",
    "page": 77,
    "chunk_index_in_page": 1,
    "text": "ve\n• Mitosis and meiosis\n• Regular distribution of chromosomes suggested that they contain hereditary informa-\ntion\n• Bridges/Morgan,usingDrosophilamelanogastershowedthatgenesareonchromosomes\n(1910s)\n• Hammerling: nucleus contains hereditary information (1930s)\n• Griffith: transformation of bacteria (1928)\n• Avery, MacLeod, McCarty: transforming substance is DNA (1944)\n• Hershey, Chase: DNA is hereditary material of viruses (1952)\n• Rosalind Franklin\n• Watson and Crick: structure of DNA (1953)\n17.3 Hershey-Chase Experiment\nThe Hershey and Chase experiment was one of the leading suggestions that DNA was a\ngenetic material. Hershey and Chase used phages, or viruses, to implant their own DNA\ninto a bacterium. They did two experiments marking either the DNA in the phage with\na radioactive phophorus or the protein of the phage with radioactive sulfur. With the\nbacteria that was infected by the phages with radioactive DNA the DNA in the bacteria\n69"
  },
  {
    "chunk_id": 153,
    "source_file": "GeneralBiology.pdf",
    "page": 78,
    "chunk_index_in_page": 0,
    "text": "DNA: The Genetic Material\nwas radioactive. In the bacteria that was infected with the radioactive protein the bacteria\nwas radioactive, not the DNA. This proves that DNA is a genetic material and it is passed\non in viruses.\n17.4 DNA/RNA components\n• Miescher: discovered DNA, 1869\n17.4.1 Structure of DNA\nDNA is in a double helix structure made up of nucleotides. The \"backbone\" of the double\nhelix is composed of phosphates connected to a five carbon sugar called deoxyribose, . The\n\"rungs\" are composed of nitrogenous bases, Purines and Pyrimidines. Purines contain\nAdenine(A) and Guanine(G) and have two rings in their structures. Pyrimidines contain\nCytosine(C) and Thymine (T) and have one ring in their structures.\n17.5 Chemical structure of DNA\n• Polynucleotide\n• Phosphodiester bonds between nucleotides\n• 5’-pGpTpCpGpTpApApTp-OH 3’\n• Chargaff’s rules, in DNA: equimolar amounts\n• A = T\n• G = C\n17.6 3D structure of DNA\n• James Watson1 and Francis Crick2 ( 19533)\n• Nucleotide"
  },
  {
    "chunk_id": 154,
    "source_file": "GeneralBiology.pdf",
    "page": 78,
    "chunk_index_in_page": 1,
    "text": "bonds between nucleotides\n• 5’-pGpTpCpGpTpApApTp-OH 3’\n• Chargaff’s rules, in DNA: equimolar amounts\n• A = T\n• G = C\n17.6 3D structure of DNA\n• James Watson1 and Francis Crick2 ( 19533)\n• Nucleotide\n• Keto and amino forms of bases\n• Chargaff’s rules\n• X-ray crystallographic data ( Rosalind Franklin4)\n17.7 Franklin\n• X-ray diffraction of DNA crystals\n• revealed regular pattern explained by antiparallel double helix\n1 http://en.wikipedia.org/wiki/James_D._Watson\n2 http://en.wikipedia.org/wiki/Francis_Crick\n3 http://en.wikipedia.org/wiki/1953\n4 http://en.wikipedia.org/wiki/Rosalind_Franklin\n70"
  },
  {
    "chunk_id": 155,
    "source_file": "GeneralBiology.pdf",
    "page": 79,
    "chunk_index_in_page": 0,
    "text": "DNA replication\nDNA model\n• Double helix of polynucleotides\n• antiparallel\n• 3’-5’ phosphodiester bonds\n• Base pairs held by hydrogen bonds\n• AT\n• GC\n• There are about 10 base pairs per turn of helix\n• model has predictive power\n• mode of DNA replication\n• encoding of genetic information\n17.8 DNA replication\n• Conservative model\n• One double helix of both old strands\n• One double helix of two new strands\n• Dispersed\n• Each strand mixture of old new\n• Semiconservative\n• Meselson-Stahl experiment confirmed its viability over the previous two\n• grew E. coli bacterium in a culture containing 15N (a heavy isotope of nitrogen)\n• bacterium assimilated the 15N into their DNA\n• a similar process was then done using 14N, a lighter isotope\n• following centrifugation, the densities were observed to be that of combined in the\nmiddle, and 14N on top, thereby confirming the semiconservative model\n17.9 DNA replication\n• Semiconservative\n• New nucleotides added to 3’ –OH\n• Replication fork"
  },
  {
    "chunk_id": 156,
    "source_file": "GeneralBiology.pdf",
    "page": 79,
    "chunk_index_in_page": 1,
    "text": "served to be that of combined in the\nmiddle, and 14N on top, thereby confirming the semiconservative model\n17.9 DNA replication\n• Semiconservative\n• New nucleotides added to 3’ –OH\n• Replication fork\n• Replication complex\n• DNA polymerase\n• Associated enzymes/proteins\n• Energy from phosphate bonds of triphosphate nucleotide substrates (dNTP)\n17.10 DNA polymerases\n• Prokaryotes, E. coli\n• 3 DNA polymerases\n• III is main enzyme for DNA replication\n• ˜1000 nt/sec\n71"
  },
  {
    "chunk_id": 157,
    "source_file": "GeneralBiology.pdf",
    "page": 80,
    "chunk_index_in_page": 0,
    "text": "DNA: The Genetic Material\n• Eukaryotes\n• 6 DNA polymerases\n• Add nucleotide to 3’ –OH end\n• All require primer, i.e., free 3’ –OH\n17.11 DNA replication complex\n• Helicase \"unzips\" the DNA double helix\n• Primase: synthesize RNA primer\n• Single-strand binding proteins\n• DNA gyrase (topoisomerase)\n• DNA polymerase III\n• DNA polymerase I (remove primer, fill gaps)\n17.12 DNA replication\n• 5’ → 3’ replication\n• Nucleotide addition at 3’ –OH\n• No exceptions\n• New strands are oriented in opposite direction due to 5’ → 3’ constraint\n• Leading strand: continuous replication\n• Lagging strand: discontinuous replication\n• contains multiple Okazaki fragments\n• Joined by DNA ligase\n17.13 DNA replication fork\n• primer required by all DNA polymerases\n17.14 Replication units\n17.15 Replicon\nA region of DNA that is replicated from a single origin.\n17.16 What is gene?\n• Garrod\n• “inborn errors of metabolism”\n• Alkaptonuria: enzyme deficiency\n72"
  },
  {
    "chunk_id": 158,
    "source_file": "GeneralBiology.pdf",
    "page": 81,
    "chunk_index_in_page": 0,
    "text": "What is gene?\n• Beadle and Tatum\n• One gene one enzyme\n• Genetic and biochemical analysis in Neurospora\n• Today: gene is sequence of nucleotides encoding functional RNA molecule or the amino\nacid sequence of a polypeptide\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n73"
  },
  {
    "chunk_id": 159,
    "source_file": "GeneralBiology.pdf",
    "page": 83,
    "chunk_index_in_page": 0,
    "text": "18 Gene expression\nFlow of genetic information\n• DNA → mRNA → polypeptide\n• Transcription: DNA → mRNA\n• RNA polymerase\n• Nucleus in eukaryotes\n• Transcription also makes rRNA and tRNA\n• Translation: mRNA → polypeptide\n• Ribosomes: protein and rRNA\n• Genetic code and tRNA\n18.1 “Central Dogma”\n18.2 The Genetic Code\n• Triplet codon\n• 64 triplet codons (43)\n• Experimentally deciphered in 1961\n• Nearly universal\n• Implies common ancestor to all living things\n• Minor exceptions: certain ciliates, mitochondria, chloroplasts\n• Still evolving\n18.3 Transcription\n• RNA polymerase\n• NTP substrates\n• Synthesizes single stranded RNA complementary to template strand of DNA\n• New nucleotides to 3’ end\n• Begins at promoter site\n• no primer necessary\n• Ends at terminator site\n• Much posttranscriptional modification in eukaryotes\n75"
  },
  {
    "chunk_id": 160,
    "source_file": "GeneralBiology.pdf",
    "page": 84,
    "chunk_index_in_page": 0,
    "text": "Gene expression\n18.4 Transcription bubble\nPromoter site\n• Prokaryotes\n• -10 nt, TATA box\n• -35 nt, additional signal\n• Eukayotes\n• -25, TATAAA box\n• Additional signals upstream\n• Promoters may be strong or weak\n• In eukaryotes, access to promoter depends upon state of chromatin coiling\n18.5 Eukaryote mRNA\n• Synthesized as pre-mRNA, processed in nucleus\n• 5’ end: GTP cap placed in inverted position\n• Essential for ribosome recognition\n• 3’ end: poly-A tail; non-templated addition of ˜50-250 A nucleotides; stability\n• Introns: intervening sequences removed\n18.6 Translation\n• Requires:\n• mRNA\n• tRNA\n• ribosomes\n• translation factors (various proteins)\n• In prokaryotes, takes place on growing mRNA\n• In eukaryotes, in cytoplasm on free ribosomes and RER\n• AUG start codon to stop codon\n18.7 Translation in bacteria\ntRNA\n• Transfer RNA\n• Two important parts\n• Anticodon\n• Hydrogen bonds with mRNA codon\n• 3’ end\n• Accepts amino acid (using energy of ATP)\n• Aminoacyl-tRNA synthetase\n76"
  },
  {
    "chunk_id": 161,
    "source_file": "GeneralBiology.pdf",
    "page": 85,
    "chunk_index_in_page": 0,
    "text": "Aminoacyl tRNA synthase\n18.8 Aminoacyl tRNA synthase\n• Enzyme used to bind amino acid from the cytoplasm to tRNA, which then transfers that\namino acid to the ribosome for polypeptide formation\n18.9 Ribosome structure\n18.10 Large ribosome subunit\n18.11 Translation\n• Initiation complex\n• Small ribosomal subunit\n• mRNA\n• fMet-tRNA (prokaryotes only; met-tRNA in eukaryotes)\n• Initiation factors\n• Elongation\n• Ribosome\n• mRNA\n• tRNAs\n• Elongation factors\n18.12 Initiation complex\n18.13 Elongation, translocation\n• incoming tRNA enters the A site\n• rRNA catalyzes peptide bond formation. Note that growing peptide is attached to what\nwas incoming tRNA at P site after translocation.\n• empty tRNA leaves via E site; recycled\n• A site ready for next charged tRNA\n18.14 Introns/exons\n• In eukaryotes, coding regions of gene may be interrupted by introns, noncoding regions\nof DNA (RNA)\n• Introns\n• 22- >10,000 nt in length\n• 5’ GU ... 3’ AG removal sequence\n• Not essential to genes"
  },
  {
    "chunk_id": 162,
    "source_file": "GeneralBiology.pdf",
    "page": 85,
    "chunk_index_in_page": 1,
    "text": "• In eukaryotes, coding regions of gene may be interrupted by introns, noncoding regions\nof DNA (RNA)\n• Introns\n• 22- >10,000 nt in length\n• 5’ GU ... 3’ AG removal sequence\n• Not essential to genes\n• May constitute >90% of gene\n77"
  },
  {
    "chunk_id": 163,
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    "page": 86,
    "chunk_index_in_page": 0,
    "text": "Gene expression\n• removed from pre-mRNA to form mRNA\n• Exon: often codes for functional domain of protein\n• translatable mRNA\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n78"
  },
  {
    "chunk_id": 164,
    "source_file": "GeneralBiology.pdf",
    "page": 87,
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    "text": "19 Gene regulation\n• Not all genes are expressed in a cell\n• Gene expression can be turned on and off\n• Multiple levels of regulation gene function\n• Transcription initiation\n• State of chromatin\n• Transcription factors\n• Post-transcriptional\n• mRNA processing\n• mRNA half-life\n• Translational\n• Post-translational\n• Protein modification\n19.1 Transcriptional control\n• State of chromatin\n• Euchromatin: transcriptionally active\n• Heterochromatin: transcriptionally inactive\n• Chemical modification of histones\n• Methylation of bases\n• Transcription factors\n• Bind to DNA at promoter or other regulatory sites (enhancers)\n• Recognize base sequence through major and minor grooves\n• Recruit RNA polymerase\n19.2 DNA grooves\nCategories of transcription factors in eukaryotes\n• Helix-turn-helix\n• Two small \"-helices\n• Fit into DNA groove\n• Homeodomain\n• Highly conserved helical domains\n• ˜60 amino acids\n• Zinc finger motif\n• Zn atom bound\n• Leucine zipper\n79"
  },
  {
    "chunk_id": 165,
    "source_file": "GeneralBiology.pdf",
    "page": 88,
    "chunk_index_in_page": 0,
    "text": "Gene regulation\n• dimer\n19.3 Regulatory proteins\n• Activity may depend upon allosteric binding of small molecules\n• cAMP\n• Co-repressors\n• Inhibitors\n• Binding to promoter region may “bend” DNA, making it accessible to other regulatory\nproteins\n19.4 Lac operon of E. coli\n• Single promoter region for cluster of genes\n• Regulated and transcribed as a single unit\n• Operons typical in prokaryotes\n• Repressor: turns OFF gene expression\nlac repressor\n• Turns off transcription by blocking access by RNA polymerase\n• repressor in activated by allosteric binding of lactose\nRegulation in eukaryotes\n• Both proximal (promoter) and distal (enhancer) to gene\n• Typically transcription unit encodes a single polypeptide\n• Promoter\n• TATA box\n• Other elements (regulatory sequences) may be present\n• Enhancers\n• Work upstream, downstream, close, far from gene\n• Bend DNA\n19.5 Alternative splicing\n• Single transcript gives rise to 2 or more mature mRNAs\n• encode different polypeptides with shared domains"
  },
  {
    "chunk_id": 166,
    "source_file": "GeneralBiology.pdf",
    "page": 88,
    "chunk_index_in_page": 1,
    "text": "ers\n• Work upstream, downstream, close, far from gene\n• Bend DNA\n19.5 Alternative splicing\n• Single transcript gives rise to 2 or more mature mRNAs\n• encode different polypeptides with shared domains\n• tissue and developmentally specific\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n(This Page was Last Edited December 2005)\n80"
  },
  {
    "chunk_id": 167,
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    "page": 89,
    "chunk_index_in_page": 0,
    "text": "20 Mutation\nA mutation is a permanent change to an organism's genetic material (DNA1 or RNA).\nMutations are a rare but significant biological process, since they provide the variation on\nwhich evolution2 acts and are also the source of cancer.\nAn organism's genetic material is made up of polymers (chains) of four different nucleotides3,\nlike a recipe book written in a language of only four letters. A mutation event is when the\norder of the nucleotides in DNA change, usually when the DNA is being copied.\nMutations come in a number of forms:\n20.1 Point Mutations\nPoint mutations are all mutations which involve a single nucleotide. These come in the form\nof substitutions, insertions and deletions:\n20.2 Substitution\nSubstitution Mutations: In substitution mutations, a nitrogenous base of a triplet codon of\nDNA is replaced by another nitrogen base or some derivative of the nitrogen base, changing\nthe codon. The altered codon codes for a different amino acid substitution.The substitution"
  },
  {
    "chunk_id": 168,
    "source_file": "GeneralBiology.pdf",
    "page": 89,
    "chunk_index_in_page": 1,
    "text": "triplet codon of\nDNA is replaced by another nitrogen base or some derivative of the nitrogen base, changing\nthe codon. The altered codon codes for a different amino acid substitution.The substitution\nmutations are of two types:\n1.Transitions: It is the replacement of one purine in a polynucleotide chain by another\npurine(A by G or C by A) or one pyrimidine by another pyrimidine(T by C or C by T)\n2.Transversions:A base pair substitution involving the substitution of a purine by pyrimidine\nor pyrimidine by a purine is called transversion.\n1 http://en.wikipedia.org/wiki/DNA\n2 http://en.wikibooks.org/wiki/General%20Biology%2FEvolution\n3 http://en.wikipedia.org/wiki/nucleotide\n81"
  },
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    "page": 90,
    "chunk_index_in_page": 0,
    "text": "Mutation\n20.2.1 Insertion\n20.2.2 Deletion\n20.3 Larger mutations\nLargermutationswhichinvolvemorethanonenucleotidealsoincludeinsertionsanddeletions,\nbut can also include inversions, rearrangement of nucleotides and duplication of entire genes:\n20.3.1 Inversion\n20.3.2 Rearrangement\n20.3.3 Gene/Exon Duplications\nTransposition\nRetrotransposition\n20.4 Chromosomal mutations\nChromosomal mutations involve changes to entire chromosomes. These mutations are\nparticularly rare:\n20.4.1 Translocation\n20.4.2 Fusion\n20.4.3 Fission\n20.4.4 Segmental Duplication\n20.4.5 Chromosomal Duplication\n20.4.6 Genome Duplication\n20.5 Causes of mutations\n20.6 Effects of mutations\nMutations can have a variety of different effects depending on the type of mutation, the\nsignificance of the piece of genetic material affected and whether the cells affected are germ-\n82"
  },
  {
    "chunk_id": 170,
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    "page": 91,
    "chunk_index_in_page": 0,
    "text": "Further reading\nline cells. Only mutations in germ-line cells can be passed on to children, while mutations\nelsewhere can cause cell-death or cancer.\nMutations can be classified by their effects:\n20.6.1 Silent Mutation\nSilent Mutations are DNA mutations that do not result in a change to the amino acid\nsequence or a protein. They may occur in a non-coding region (outside of a gene or within\nan intron), or they may occur within an exon in a manner that does not alter the final\namino acid chain.\n20.6.2 Frameshift\n20.6.3 Missense Mutation\nMissense mutations are types of point mutations where a single nucleotide is changed to\ncause substitution of a different amino acid. This in turn can render the resulting protein\nnonfunctional. Such mutations are responsible for diseases such as Epidermolysis bullosa.\n20.6.4 Nonsense Mutation\n20.7 Further reading\n20.7.1 Books\n• Jones, S. 1993. The Language of the Genes. Harper Collins ISBN 0006552439.\n20.7.2 Websites\n• Wikipedia: Mutation4"
  },
  {
    "chunk_id": 171,
    "source_file": "GeneralBiology.pdf",
    "page": 91,
    "chunk_index_in_page": 1,
    "text": "s Epidermolysis bullosa.\n20.6.4 Nonsense Mutation\n20.7 Further reading\n20.7.1 Books\n• Jones, S. 1993. The Language of the Genes. Harper Collins ISBN 0006552439.\n20.7.2 Websites\n• Wikipedia: Mutation4\n• http://www.evowiki.org/Mutation\n20.8 Original notes\n• “Rare” change in nucleotide sequence\n• Somatic vs germline\n• only those in germline are heritable\n• Point mutation\n• Single nucleotide change\n• Change in gene position\n4 http://en.wikipedia.org/wiki/Mutation\n83"
  },
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    "chunk_id": 172,
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    "page": 92,
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    "text": "Mutation\n• Transposition\n• Chromosomal rearrangement\n• Mutagenic agents\n• Raw material for evolutionary change\n20.9 Point mutation\n• Ionizing radiation\n• UV light induces thymine dimers\n• Reparable\n• Error during DNA synthesis\n• Movement of transposons\n• McClintock\n• Chemical mutagens\n• May alter\n• Properties of promoter, enhancer\n• Amino acid sequence of polypeptide\n20.10 Acquisition of genetic variability\n• Mutation\n• Sex (fusion of genomes)\n• Recombination\n• Crossing over\n• Reciprocal (may result in gene conversion)\n• Unequal (gives rise to gene families)\n• Independent segregation\n• Transposition by transposons\n• Conjugation in bacteria\n• One way transfer from donor to recipient\n20.11 Eukaryote genome\n• Thousands of transposons\n• Millions of transposon derived elements\n• LINES, SINES\n• Above may constitute largest portion of genome\n• Pseudogenes\n• Tandem clusters (rRNA genes; nucleolus)\n• Multigene families\n• Single-copy genes (one copy per 1n)\n84"
  },
  {
    "chunk_id": 173,
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    "page": 93,
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    "text": "Barbara McClintock\n20.12 Barbara McClintock\n• Discovered transposons in perhaps greatest and ultimately most important intellectual\nendeavors in genetics\n• Maize\n• Worked alone\n• Transposons: likely responsible for considerable evolution in eukaryotic genomes\n• Likely origin of viruses\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n85"
  },
  {
    "chunk_id": 174,
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    "page": 95,
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    "text": "21 Recombinant DNA technology\n• Revolutionized modern biology\n• Ability to manipulate genes in vitro\n• Hybrid genes, including combining genes of different species\n• Detailed study of gene function\n• Determine nucleotide sequences of genes and their regulators (deduce amino acid\nsequences of proteins)\n• Genome projects: complete nucleotide sequence of >40 genomes, including human\n• Made possible by convergence of:\n• discovery of restriction enzymes\n• genetics of bacteria and their plasmids\n21.1 Recombinant DNA technology\n• Uses\n• Detailed study of gene function\n• Homeostasis, response to stress\n• Development (birth defects)\n• Evolution of genes informs on evolution of life\n• Human betterment\n• Medicine\n• Identification, treatment of genetic disorders\n• Molecular medicine: from deduced amino acid sequences, design better drugs\n• Foods\n• Improve crop yield, resistance to disease\n• Improve nutritional value\n• Forensics\n• DNA fingerprinting: guilt or innocence"
  },
  {
    "chunk_id": 175,
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    "page": 95,
    "chunk_index_in_page": 1,
    "text": "r medicine: from deduced amino acid sequences, design better drugs\n• Foods\n• Improve crop yield, resistance to disease\n• Improve nutritional value\n• Forensics\n• DNA fingerprinting: guilt or innocence\n21.2 Restriction endonucleases\nOriginally found in bacteria to prevent invasion of viral DNA, cuts double stranded DNA\nthat is unmethylated, will not cut newly synthesized DNA since hemi-methylated, a product\nof semi-conservative replication of DNA\n• sever phosphodiester bonds of both polynucleotide strands in order to combine foreign\nDNA\n• create restriction fragments (restriction digestion)\n• 5’ phosphate and 3’ –OH at ends\n87"
  },
  {
    "chunk_id": 176,
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    "page": 96,
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    "text": "Recombinant DNA technology\n• usually nucleotide specific target sequence\n• 4-6 bp most common, the more bases, then the more specific for recombination\n• cuts in or near sequence\n• ends\n• sticky=overhanging ends, 5’ or 3’\n• blunt ends - straight cut, will anneal with any other blunt end in the presence of high\nligase\n• Hundreds of know restriction endonucleases, usually named after the bacteria that it was\nfound in\n• e.g. EcoR1, Alu1, BAM, HIND3\n21.3 Restriction endonucleases\nGene cloning\n• Cloning:\n• Restriction digestion of DNA\n• insertion of restriction fragment into cloning vector\n• Bacterial plasmid\n• Bacterial virus\n• Yeast artificial chromosomes\n• Transformation of bacteria with recombinant plasmid, virus\n• Screening for clone of interest by using reporter genes or resistance upon exposure to\nanti-biotic\n21.4 Uses of cloned gene\n• Determine nucleotide sequence and deduce amino acid sequence from genetic code\n• Submit to GenBank (available on WWW)"
  },
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    "page": 96,
    "chunk_index_in_page": 1,
    "text": "orter genes or resistance upon exposure to\nanti-biotic\n21.4 Uses of cloned gene\n• Determine nucleotide sequence and deduce amino acid sequence from genetic code\n• Submit to GenBank (available on WWW)\n• Manipulate gene to study function\n• In vitro\n• In vivo\n• Transgenic (recombinant) organisms\n• Knockout organisms\n• Medical and commercial uses\n21.5 Other molecular procedures\n• Polymerase chain reaction (Mullis)\n• Amplifies target DNA without cloning\n• Target amount can be single molecule\n• Amplified DNA can be sequenced, cloned, etc.\n• Southern blotting\n• Used to identify restriction fragments carrying particular gene\n88"
  },
  {
    "chunk_id": 178,
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    "page": 97,
    "chunk_index_in_page": 0,
    "text": "RFLP(restriction fragment length polymorphism) analysis\n• Also used for DNA fingerprinting and RFLP analysis\n• cDNA construction\n• Reverse transcription from mRNA template\n21.6 RFLP(restriction fragment length polymorphism)\nanalysis\n• Basis of DNA fingerprinting using SNP - single nucleotide polymorphisms and repeats of\nDNA sequence\n• Many uses\n• Criminal cases using multiple probes\n• Parentage\n• Species identification\n• Gene evolution\n• Species evolution\n21.7 Sanger DNA sequencing\n• Uses dideoxynucleotides (ddNTP), a template strand, DNA polymerase 1 (Also known\nas Kornberg enzymes) and dNTPs\n• Missing 3’-OH for nulceopjilic attack for elongation\n• DNA synthesis stops after one is incorporated into DNA fragment\n• ratio of ddNTP to dNTP determines likelihood of termination\n• Manual method with 32P-labeled ddATP and 4 test tubes - ddATP, ddCTP, ddGTP,\nddTTP\n• Automated method using ddNTPs labeled with fluorescent dyes in capillary tube\n• Often done commercially"
  },
  {
    "chunk_id": 179,
    "source_file": "GeneralBiology.pdf",
    "page": 97,
    "chunk_index_in_page": 1,
    "text": "mination\n• Manual method with 32P-labeled ddATP and 4 test tubes - ddATP, ddCTP, ddGTP,\nddTTP\n• Automated method using ddNTPs labeled with fluorescent dyes in capillary tube\n• Often done commercially\n21.8 Automated sequencing\nTypical machine\n• • 2 hour sequencing run\n• 600-1000 bases per sample\n• multiple samples\n• Up to 500,000 bases per day (12 hr)\n• Data processed by computer\n• In big labs, sequencing reactions also are automated\n21.9 Genome projects\n• Determine entire nucleotide sequence of genome\n89"
  },
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    "page": 98,
    "chunk_index_in_page": 0,
    "text": "Recombinant DNA technology\n• >40 genomes sequenced\n• Helicobacter pylori\n• Escherichia coli\n• Saccharomyces cerevisiae\n• Caenorhabditis elegans\n• Drosophila melanogaster\n• Homo sapiens (first rough draft)\n• Computer identifies all genes, based on properties of genes (e.g., start/stop codons,\nintrons, etc.).\n21.10 Biochips\n• Microarray of DNA fragments, size of postage stamp; can be expensive, but has decreased\nin cost\nMicroarray chips contain wells of DNA that code for specific genes that uses the concept of\nhybridization with the gene of interest to see if a gene is expressed or is present.\n• Designed to detect:\n• mutated genes (SNPs)\n• expressed genes\n• Instant DNA profile (“GATTACA”)\n21.11 DNA chip controversies\n• Medicine\n• Risks and informed consent for gene replacement therapy\n• Alteration of human gene pool\n• Parental choice\n• Privacy\n• Genetically modified foods\n• Safety\n• Labeling\n• Forensics\n• Mandatory tests\n• Reliability standards\n21.12 Gene patenting"
  },
  {
    "chunk_id": 181,
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    "page": 98,
    "chunk_index_in_page": 1,
    "text": "acement therapy\n• Alteration of human gene pool\n• Parental choice\n• Privacy\n• Genetically modified foods\n• Safety\n• Labeling\n• Forensics\n• Mandatory tests\n• Reliability standards\n21.12 Gene patenting\n• Techniques to study and manipulate genes are patented (e.g., cloning and PCR)\n• Should genes be patented?\n• Are they the intellectual property of the discoverer?\n• Don’t they belong to all of us?\n• Should indigenous peoples be compensated for useful genes extracted from their local\nplants and fungi?\n90"
  },
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    "page": 99,
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    "text": "Stem cells\n21.13 Stem cells\n• Totipotent cells from early embryo\n• grow into any tissue or cell type\n• Recombinant genes can be introduced\n• Considerable use in analyzing gene expression in mice\n• Possible therapeutic use in humans\n• Very controversial\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n91"
  },
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    "page": 101,
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    "text": "22 Classification of Living Things\n22.0.1 Classification of Living Things & Naming\nWith so many flora and fauna on planet Earth, there must be a method to classify each\norganism to distinguish it from others so it can be correctly identified. Classification does\nnot only apply to biology. For example, supermarkets and grocery stores organise their\nproducts by classifying them. Beverages may occupy one aisle, while cleaning supplies may\noccupy another. In science, the practice of classifying organisms is called taxonomy (Taxis\nmeans arrangement and nomos means law). The modern taxonomic system was developed\nby the Swedish botanist Carolus (Carl) Linneaeus (1707-1788). He used simple physical\ncharacteristics of organisms to identify and differentiate between different species.\nLinneaeus developed a hierarchy of groups for taxonomy. To distinguish different levels of\nsimilarity, each classifying group, called taxon (pl. taxa) is subdivided into other groups."
  },
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    "page": 101,
    "chunk_index_in_page": 1,
    "text": "ferent species.\nLinneaeus developed a hierarchy of groups for taxonomy. To distinguish different levels of\nsimilarity, each classifying group, called taxon (pl. taxa) is subdivided into other groups.\nTo remember the order, it is helpful to use a mnemonic device. The taxa in hierarchical\norder:\n• Domain - Archea, Eubacteria, Eukaryote\n• Kingdom - Plants, Animals, Fungi, Protists, Eubacteria (Monera), Archaebacteria\n• Phylum\n• Class\n• Order\n• Family\n• Genus\n• Species\nThe domain is the broadest category, while species is the most specific category available.\nThe taxon Domain was only introduced in 1990 by Carl Woese, as scientists reorganise\nthings based on new discoveries and information. For example, the European Hare would\nbe classified as follows:\nEukaryote --> Animal --> Chordata --> Mammalia --> Lagomorpha --> Leporidae -->\nLepus --> Lepus europaeus.\nBinomial nomenclature is used to name an organism, where the first word beginning"
  },
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    "page": 101,
    "chunk_index_in_page": 2,
    "text": "s follows:\nEukaryote --> Animal --> Chordata --> Mammalia --> Lagomorpha --> Leporidae -->\nLepus --> Lepus europaeus.\nBinomial nomenclature is used to name an organism, where the first word beginning\nwith a capital is the genus of the organism and the second word beginning with lower-case\nletter is the species of the organism. The name must be in italics and in Latin, which was\nthe major language of arts and sciences in the 18th century. The scientific name can be also\nabbreviated, where the genus is shortened to only its first letter followed by a period. In our\nexample, Lepus europaeus would become L. europaeus'.\nTaxonomy and binomial nomenclature are both specific methods of classifying an organism.\nThey help to eliminate problems, such as mistaken identity and false assumptions, caused\nby common names. An example of the former is the fact that a North American robin is\n93"
  },
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    "page": 102,
    "chunk_index_in_page": 0,
    "text": "Classification of Living Things\nquite different from the English robin. An example of the latter is the comparison between\ncrayfish and catfish, where one might believe that they both are fish when in fact, they are\nquite different.\nNomenclature is concerned with the assignment of names to taxonomic groups in agreement\nwith published rules.\n22.0.2 Eukaryotes & Prokaryotes\nRecall that there are two basic types of cells: eukaryotes and prokaryotes.\nEukaryotes are more complex in structure, with nuclei and membrane-bound organelles.\nSome characteristics of eukaryotes are:\n• Large (100 - 1000 μm)\n• DNA in nucleus, bounded by membrane\n• Genome consists of several chromosomes.\n• Sexual reproduction common, by mitosis and meiosis\n• Mitochondria and other organelles present\n• Most forms are multicellular\n• Aerobic\nProkaryotes refer to the smallest and simplest type of cells, without a true nucleus and no\nmembrane-bound organelles. Bacteria fall under this category. Some characteristics:"
  },
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    "page": 102,
    "chunk_index_in_page": 1,
    "text": "multicellular\n• Aerobic\nProkaryotes refer to the smallest and simplest type of cells, without a true nucleus and no\nmembrane-bound organelles. Bacteria fall under this category. Some characteristics:\n• Small (1-10 μm)\n• DNA circular, unbounded\n• Genome consists of single chromosome.\n• Asexual reproduction common, not by mitosis or meiosis.\n• No general organelles\n• Most forms are singular\n• Anaerobic\n22.0.3 The Three Domains\nThe three domains are organised based on the difference between eukaryotes and prokaryotes.\nToday's living prokaryotes are extremely diverse and different from eukaryotes. This fact has\nbeen proven by molecular biological studies (e.g. of RNA structure) with modern technology.\nThe three domains are as follows:\nArchea (Archeabacteria) consists of archeabacteria, bacteria which live in extreme\nenvironments. The kingdom Archaea belongs to this domain.\nEubacteriaconsistsofmoretypicalbacteriafoundineverydaylife. ThekingdomEubacteria\nbelongs to this domain."
  },
  {
    "chunk_id": 188,
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    "page": 102,
    "chunk_index_in_page": 2,
    "text": "eria, bacteria which live in extreme\nenvironments. The kingdom Archaea belongs to this domain.\nEubacteriaconsistsofmoretypicalbacteriafoundineverydaylife. ThekingdomEubacteria\nbelongs to this domain.\nEukaryote encompasses most of the world's visible living things. The kingdoms Protista,\nFungi, Plantae, and Animalia fall under this category.\n94"
  },
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    "text": "Stem cells\n22.0.4 The Six Kingdoms\nUnderthethreedomainsaresixkingdomsintaxonomy. Thefirsttwo, PlantsandAnimals,\nare commonly understood and will not be expounded here.\nProtista, the third kingdom, was introduced by the German biologist Ernst Haeckel in\n1866 to classify micro-organisms which are neither animals nor plants. Since protists are\nquite irregular, this kingdom is the least understood and the genetic similarities between\norganisms in this kingdom are largely unknown. For example, some protists can exhibit\nproperties of both animals and plants.\nFungi are organisms which obtain food by absorbing materials in their bodies. Mushrooms\nand moulds belong in this kingdom. Originally, they were part of the plant kingdom but\nwere recategorised when they were discovered not to photosynthesise.\nEubacteria are bacteria, made up of small cells, which differ in appearance from the\norganisms in the above kingdoms. They lack a nucleus and cell organelles. They have cell"
  },
  {
    "chunk_id": 190,
    "source_file": "GeneralBiology.pdf",
    "page": 103,
    "chunk_index_in_page": 1,
    "text": "d not to photosynthesise.\nEubacteria are bacteria, made up of small cells, which differ in appearance from the\norganisms in the above kingdoms. They lack a nucleus and cell organelles. They have cell\nwalls made of peptidoglycan.\nArchae (or Archaebacteria) are bacteria which live in extreme environments, such as\nsalt lakes or hot, acidic springs. These bacteria are in their own category as detailed studies\nhave shown that they have unique properties and features (ex. unusual lipids that are not\nfound in any other organism)which differ them from other bacteria and which allow them to\nlive where they live. Their cell walls lack peptidoglycan.\n22.0.5 Origins of Diversity\nThe diversity in our planet is attributed to diversity within a species. As the world changed\nin climate and in geography as time passed, the characteristics of species diverged so much\nthat new species were formed. This process, by which new species evolve, was first described"
  },
  {
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    "source_file": "GeneralBiology.pdf",
    "page": 103,
    "chunk_index_in_page": 2,
    "text": "world changed\nin climate and in geography as time passed, the characteristics of species diverged so much\nthat new species were formed. This process, by which new species evolve, was first described\nby British naturalist Charles Darwin as natural selection.\nFor an organism to change, genetic mutations must occur. At times, genetic mutations are\naccidental, as in the case of prokaryotes when they undergo asexual reproduction. For most\neukaryotes, genetic mutations occur through sexual reproduction, where meiosis produces\nhaploid gametes from the original parent cells. The fusion of these haploid gametes into\na diploid zygote results in genetic variation in each generation. Over time, with enough\narrangement of genes and traits, new species are produced. Sexual reproduction creates an\nimmense potential of genetic variety.\nOne goal of taxonomy is to determine the evolutionary history of organisms. This can be\nachieved by comparing species living today with species in the past."
  },
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    "page": 103,
    "chunk_index_in_page": 3,
    "text": "es an\nimmense potential of genetic variety.\nOne goal of taxonomy is to determine the evolutionary history of organisms. This can be\nachieved by comparing species living today with species in the past. The comparison in\nanatomy and structure is based on data from development, physical anatomy, biochemistry,\nDNA, behaviour, and ecological preferences. The following are examples of how such data is\nused:\n• Anatomy:\nAlthough a horse and a human may look different, there is evidence that their arm structures\nare quite similar. Their arms' sizes and proportions may be different, but the anatomical\nstructures are quite similar. Such evidence reveals that animals in different taxa may not\n95"
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    "page": 104,
    "chunk_index_in_page": 0,
    "text": "Classification of Living Things\nbe that different. Biological features from a common evolutionary origin are known as\nhomologous.\n• Development\n• Biochemistry:\nBiochemical analysis of animals similar in appearance have yielded surprising results. For\nexample, although guinea pigs were once considered to be rodents, like mice, biochemistry\nled them to be in their taxon of their own.\n22.0.6 Phylogeny, Cladistics & Cladogram\nModern taxonomy is based on many hypotheses' of the evolutionary history of organisms,\nknown as phylogeny. As with the Scientific Method, scientists develop a hypothesis on the\nhistory of an animal and utilise modern science and technology to prove the phylogeny.\nCladistics is a classification system which is based on phylogeny. Expanding on phylogeny,\ncladistics is based on the assumption that each group of related species has one common\nancestor and would therefore retain some ancestral characteristics. Moreover, as these"
  },
  {
    "chunk_id": 194,
    "source_file": "GeneralBiology.pdf",
    "page": 104,
    "chunk_index_in_page": 1,
    "text": "Expanding on phylogeny,\ncladistics is based on the assumption that each group of related species has one common\nancestor and would therefore retain some ancestral characteristics. Moreover, as these\nrelated species evolve and diverge from their common ancestor, they would develop unique\ncharacteristics. Such characteristics are known as derived characteristics\nThe principles of phylogeny and cladistics can be expressed visually as a cladogram,\na branching diagram which acts as a family (phylogenetic) tree for similar species. A\ncladogram can also be used to test alternative hypotheses for an animal's phylogeny. In\norder to determine the most likely cladogram, the derived characteristics of similar species\nare matched and analysed.\n22.0.7 Classification of Living Things Practice Questions\n1. If taxonomists had to select an existing kingdom to reclassify, which of the six would\nmost likely be chosen? Why?\n2. Complete the following without consulting external sources:"
  },
  {
    "chunk_id": 195,
    "source_file": "GeneralBiology.pdf",
    "page": 104,
    "chunk_index_in_page": 2,
    "text": "Practice Questions\n1. If taxonomists had to select an existing kingdom to reclassify, which of the six would\nmost likely be chosen? Why?\n2. Complete the following without consulting external sources:\na) The species caudatum is in the family Paramecidae. What would be the binomial name\nof this organism?\nb) Give the abbreviation of the binomial name.\n3.\na) Irish moss belongs to the genus Chondrus. The name for this species is crispus. Give the\nbinomial name.\nb) Give the abbreviation of the binomial name.\n4. Humans and chimpanzees are alike. Which of the following data would most accurately\nprove this correct?\na) biochemistry\n96"
  },
  {
    "chunk_id": 196,
    "source_file": "GeneralBiology.pdf",
    "page": 105,
    "chunk_index_in_page": 0,
    "text": "Introduction\nb) DNA\nc) appearance\nd) development\ne) A, B, C\n5. Which of the following is out of order?\na) Kingdom --> Phyllum --> Class\nb) Class --> Family --> Order\nc) Family --> Order --> Genus\nd) Genus --> Species\ne) A, C\nf) A, B, D\ng) B, C\n6. A taxonomist discovers Organism A and Organism B and wishes to classify them. Which\nof the following choices is the most informative?\na) Both organisms are brown.\nb) Both organisms have a tail.\nc) Both organisms have ears.\nd) Both organisms are nocturnal.\n7. DNA analysis is usually done using DNA found in a cell's mitochondria, and not in a\ncell's nucleus. From your knowledge of mitosis, explain why this is so.\n1. Arachbacteria 3.a) Chondrus crispus b) C. cripus 4. B 5. G 6. B\n22.1 Introduction\nVirusesarethesmallestbiologicalparticle(thetiniestareonly20nmindiameter). However,\nthey are not biological organisms so they are not classified in any kingdom of living things."
  },
  {
    "chunk_id": 197,
    "source_file": "GeneralBiology.pdf",
    "page": 105,
    "chunk_index_in_page": 1,
    "text": "6. B\n22.1 Introduction\nVirusesarethesmallestbiologicalparticle(thetiniestareonly20nmindiameter). However,\nthey are not biological organisms so they are not classified in any kingdom of living things.\nThey do not have any organelles and cannot respire or perform metabolic functions. Viruses\nare merely strands of DNA or RNA surrounded by a protective protein coat called a capsid.\nViruses only come to life when they have invaded a cell. Outside of a host cell, viruses are\ncompletely inert.\nSince first being identified in 1935, viruses have been classified into more than 160 major\ngroups. Viruses are classified based on their shape, replication properties, and the diseases\nthattheycause. Furthermore,theshapeofavirusisdeterminedbythetypeandarrangement\nof proteins in its capsid. Viruses pathogenic to humans are currently classified into 21 groups.\nViruses can also attack bacteria and infect bacterial cells. Such viruses are called bacterio-\nphages.\n97"
  },
  {
    "chunk_id": 198,
    "source_file": "GeneralBiology.pdf",
    "page": 106,
    "chunk_index_in_page": 0,
    "text": "Classification of Living Things\n22.2 Viral Replication\nAs previously stated, viruses are not a biological life form so they cannot reproduce by\nthemselves. They need to take over a functioning eukaryotic or prokaryotic cell to replicate\nits DNA or RNA and to make protein coat for new virus particles.\nInordertoenteracell,avirusmustattachtoaspecificreceptorsiteontheplasmamembrane\nof the host cell. The proteins on the surface of the virus act as keys which fit exactly into a\nmatching glycoprotein on the host cell membrane. In some viruses, the attachment protein\nis not on the surface of the virus but is in the capsid or in the envelope.\nThere are two forms of viral replication: the lytic cycle and the lysogenic cycle.\n22.2.1 Lytic Cycle\n1. Attachment: The virus binds to specific receptors on the host cell.\n2. Entry: There are two ways in which a virus can enter cells. Firstly, the virus can inject\nits nucleic acid into the host cell. Secondly, if a virus is contained in an envelope, the"
  },
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    "source_file": "GeneralBiology.pdf",
    "page": 106,
    "chunk_index_in_page": 1,
    "text": "the host cell.\n2. Entry: There are two ways in which a virus can enter cells. Firstly, the virus can inject\nits nucleic acid into the host cell. Secondly, if a virus is contained in an envelope, the\nhost cell can phagocytosise the entire virus particle into a vacuole. When the virus\nbreaks out of the vacuole, it then releases its nucleic acid into the cell.\n3. Replication: The virus's nucleic acid instructs the host cell to replicate the virus's\nDNA or RNA.\n4. Assembly: New virus particles are assembled.\n5. Lysis and Release: The virus directs the production of an enzyme which damages\nthe host cell wall, causing the host cell to swell and burst. The newly formed virus\nparticles are now released.\n22.2.2 Lysogenic Cycle\n1. Attachment: Similar to Lytic Cycle\n2. Entry: Similar to Lytic Cycle\n3. Incorporation: The viral nucleic acids is not replicated, but instead integrated by\ngenetic combination (crossing over) into the host cell's chromosome. When integrated"
  },
  {
    "chunk_id": 200,
    "source_file": "GeneralBiology.pdf",
    "page": 106,
    "chunk_index_in_page": 2,
    "text": "try: Similar to Lytic Cycle\n3. Incorporation: The viral nucleic acids is not replicated, but instead integrated by\ngenetic combination (crossing over) into the host cell's chromosome. When integrated\nin a host cell this way, the viral nucleic acid as part of the host cell's chromosome is\nknown as a prophage.\n4. Host Cell Reproduction: The host cell reproduces normally. Subsequent cell divisions,\ndaughter cells, contain original father cell's chromosome embedded with a prophage.\n5. Cycle Induction: Certain factors now determine whether the daughter cell undergoes\nthe lytic or lysogenic cycle. At any time, a cell undergoing the lysogenic cycle can\nswitch to the lytic cycle.\nThe reproduction cycle of viruses with RNA and no DNA is slightly different. A notable\nexample of a RNA-based virus is HIV, a retrovirus.\n98"
  },
  {
    "chunk_id": 201,
    "source_file": "GeneralBiology.pdf",
    "page": 107,
    "chunk_index_in_page": 0,
    "text": "Viral Genome\nRetrovirus reproductive cycle\n1. The retrovirus force RNA into cell, by either one of the two methods of entry (See\nabove).\n2. In the retrovirus are reverse transcriptase enzymes, which catalyses the synthesis of a\nDNA strand complementary to the viral RNA.\n3. Reverse transcriptase catalyses a second DNA strand complementary to the first. With\nthese two strands, the double-stranded DNA can be created.\n4. DNA is then incorporated into the host cell's chromosomes. Similar to the concept of\na prophage, this incorporated DNA is called a provirus. However, the provirus never\nleaves the host cell, unlike a prophage.\n5. The infected host cell undergoes the lytic or lysogenic cycle.\n22.3 Viral Genome\nThe genome of a virus consists of DNA or RNA, whose size and configuration vary. The\nentire genome can exist as a single nucleic acid molecule or several nucleic acid segments.\nAlso, the DNA or RNA may be single-stranded or double-stranded, and either linear or\ncircular."
  },
  {
    "chunk_id": 202,
    "source_file": "GeneralBiology.pdf",
    "page": 107,
    "chunk_index_in_page": 1,
    "text": "on vary. The\nentire genome can exist as a single nucleic acid molecule or several nucleic acid segments.\nAlso, the DNA or RNA may be single-stranded or double-stranded, and either linear or\ncircular.\nNot all viruses can reproduce in a host cell by themselves. Since viruses are so small, the\nsize of their genome is limiting. For example, some viruses have coded instructions for only\nmaking a few different proteins for the viruses' capsid. On the other hand, the human\ngenome codes for over 30,000 different proteins. Therefore, the lack of coded instructions\ncause some viruses to need the presence of other viruses to help them reproduce themselves.\nSuch viruses are called replication defective.\nLastly, it is worthy to note that 70% of all viruses are RNA viruses. As the process of RNA\nreplication (with enzymes and other organelles of the host cell) is more prone to errors, RNA\nviruses have much higher mutation rates than do DNA viruses.\n22.4 Viruses Practice Questions\n1."
  },
  {
    "chunk_id": 203,
    "source_file": "GeneralBiology.pdf",
    "page": 107,
    "chunk_index_in_page": 2,
    "text": "ess of RNA\nreplication (with enzymes and other organelles of the host cell) is more prone to errors, RNA\nviruses have much higher mutation rates than do DNA viruses.\n22.4 Viruses Practice Questions\n1. As the name implies, the Tomato Spotted Wilt Virus targets tomatoes. Would it be\npossible for this virus to target other fruits as well? Explain.\n2. If a DNA and a RNA virus both infected somatic cells, which virus would be more\ndifficult to detect?\n3. Many people have had cold sores, which are caused by infection with the herpes\nsimplex virus. One characteristic of cold sores is that after a period of inactivity, they\nwill reappear many times during the course of a person's life. Which cycle would the\nherpes simplex virus undergo?\n4. Chicken pox is a common, non-fatal disease usually acquired in adolescence and caused\nby the varicella zoster virus. In adulthood, many people suffer from shingles, an altered\nform of the varicella zoster virus."
  },
  {
    "chunk_id": 204,
    "source_file": "GeneralBiology.pdf",
    "page": 107,
    "chunk_index_in_page": 3,
    "text": "is a common, non-fatal disease usually acquired in adolescence and caused\nby the varicella zoster virus. In adulthood, many people suffer from shingles, an altered\nform of the varicella zoster virus. Which cycle would the varicella zoster virus have\nundergone?\n5. Would an antibiotic work for a person suffering from a cold of flu? Explain.\n99"
  },
  {
    "chunk_id": 205,
    "source_file": "GeneralBiology.pdf",
    "page": 108,
    "chunk_index_in_page": 0,
    "text": "Classification of Living Things\nAnswers to Viruses Practice Questions1\nFor Eubacteria, please visit General Biology/Classification of Living Things/Eubacteria2.\n22.5 Archaea\n• Proposed as separate group from (eu)bacteria by Carl Woese\n• based on structure and metabolic pathways\n• inhabit extreme environments\n• unique branched lipids in membrane\n• Share traits with both eukaryotes and eubacteria, e.g., RNA polymerase, introns\n• Biochemically diverse\n• Economically important\n• Taq polymerase used in PCR\n22.5.1 Types\n• Methanogens\n• Halophiles\n• Thermophiles\nUnderground bacteria\n• Metabolism\n• built around inorganic energy sources\n• e.g., basalt reacts with H O to release hydrogen which is catalytically combined with\n2\nCO to form carbohydrate (akin to photosynthesis)\n2\n• may result in deposit of minerals\n• Unresolved problems\n• Did bacteria move downward from surface or did they first evolve there, protected\nfrom harsh surface conditions?\n• Could bacteria be ejected into space in rocks?"
  },
  {
    "chunk_id": 206,
    "source_file": "GeneralBiology.pdf",
    "page": 108,
    "chunk_index_in_page": 1,
    "text": "t of minerals\n• Unresolved problems\n• Did bacteria move downward from surface or did they first evolve there, protected\nfrom harsh surface conditions?\n• Could bacteria be ejected into space in rocks?\n22.6 Prokaryote evolution\n• Tentative, subject to change\n• Derived largely from molecular systematics (rRNA sequences)\n• Note: most bacteria can’t be cultured, thus hard to study! (Studied by PCR of water/soil\nsamples)\n1 http://en.wikibooks.org/wiki/%2FAnswers\nhttp://en.wikibooks.org/wiki/General%20Biology%2FClassification%20of%20Living%\n2\n20Things%2FEubacteria\n100"
  },
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    "chunk_id": 207,
    "source_file": "GeneralBiology.pdf",
    "page": 109,
    "chunk_index_in_page": 0,
    "text": "Domains of life: characteristics\n22.7 Domains of life: characteristics\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n22.8 Introduction\nOut of the six kingdoms, Protista is the most diverse. This is the kingdom of organisms\nwith strange, atypical characteristics. In essence, this kingdom is designated for organisms\nwhich do not belong in any other kingdom. The majority of protists are microscopic.\n22.9 Classification of Protists\nThere are three phyla of protists, based on their type of nutrition.\n1. Protozoa (animal-like protists) are heterotrophs that ingest or absorb their food.\n2. Algae (plant-like protists) are autotrophs they get nutrition from photosythesis.\n3. Slime moulds and water moulds (fungus-like protists) are also heterotrophs, like\nprotozoa.\n22.10 Protozoa\nAs heterotrophs, protozoa scavenge materials from their surroundings. Others are predators"
  },
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    "chunk_id": 208,
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    "page": 109,
    "chunk_index_in_page": 1,
    "text": "3. Slime moulds and water moulds (fungus-like protists) are also heterotrophs, like\nprotozoa.\n22.10 Protozoa\nAs heterotrophs, protozoa scavenge materials from their surroundings. Others are predators\nwhich actively hunt or ambush small organisms such as bacteria and other protozoa for a\nsource of nutrition. Protozoa can be parasitic as well; they may live inside larger organisms,\nlike humans. Most protozoa live as single cells, although a few form colonies.\nProtozoa are generally difficult to identify due to their varied shape. They may appear as\njelly-like blobs, spherical sunbursts, or a flattened leaf. Tiny blood parasites may be only 2\nμm long. On the other hand, shell-covered marine may be 5 cm or more in diameter.\nFurthermore, different protozoans have their own complex life cycles. The complexity has\nled certain organisms to be mistakenly classified for other species.\nNevertheless, protozoa can move, and so, they are classified based on their methods of\nlocomotion."
  },
  {
    "chunk_id": 209,
    "source_file": "GeneralBiology.pdf",
    "page": 109,
    "chunk_index_in_page": 2,
    "text": "life cycles. The complexity has\nled certain organisms to be mistakenly classified for other species.\nNevertheless, protozoa can move, and so, they are classified based on their methods of\nlocomotion.\nCharacteristics of Protozoa :\n• About 30,000 species known\n• About 10,000 species are pathogenic, including some of the worst human diseases\n• heterotrophic\n• highly variable in form and life cycle\n101"
  },
  {
    "chunk_id": 210,
    "source_file": "GeneralBiology.pdf",
    "page": 110,
    "chunk_index_in_page": 0,
    "text": "Classification of Living Things\n• mostly unicellular\n• range in size from 0.005 mm to 50 mm\n• lack cell walls\nthey love environment and each other..............\n22.11 Algae\nAlgae are much simpler than protozoa. They are aquatic and contain chlorophyll. Algae can\nexist as a single cell or as giant seaweeds 60 m in length. Formerly, algae were classified as\nplants but this was incorrect as algae lack parts of true plants: leaves, stems, roots, xylem,\nand phloem. Since algae belong in the kingdom Protista, algae is a broad term used to\ndenote all aquatic eukaryotes which photosynthesise; algae can differ in size and shape as\nwell.\nThere are six phyla of algae:chlorophytes (green algae), phaeophytes (brown algae),\nrhodophytes (red algae), chrysophytes (diatoms), pyrrophytes (dinoflagellates),\nand euglenophytes (euglenoids).\n22.11.1 Chlorophytes\nChlorophytes resemble plants the most. Like plants, their cell walls contain cellulose and\nthey store food in reserve as starch."
  },
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    "chunk_index_in_page": 1,
    "text": "(dinoflagellates),\nand euglenophytes (euglenoids).\n22.11.1 Chlorophytes\nChlorophytes resemble plants the most. Like plants, their cell walls contain cellulose and\nthey store food in reserve as starch. Chlorophytes can be unicellular or multicellular. Most\nchlorophytes use flagellae for some locomotion.\n22.11.2 Phaeophytes\nPhaeophytesarenearlyallmulticellularmarineorganisms,whichareknowntousasseaweeds.\nThey have cell walls composed of cellulose and alginic acid (a substance similar to pectin).\nThe cellulose and alignic acid help to retain water and prevent seawood from drying out\nwhen exposed to air at low tide.\nSince phaeophytes live in a tidal environment, they have large, flat fronds (a large leaf)\nwhich can withstand pounding by waves. Their bases strongly anchor the algae to the rocky\nseabed and prevent them from being washed out to sea. Phaeophytes are usually found in\nareas of cold water.\n22.11.3 Rhodophytes"
  },
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    "chunk_id": 212,
    "source_file": "GeneralBiology.pdf",
    "page": 110,
    "chunk_index_in_page": 2,
    "text": "d pounding by waves. Their bases strongly anchor the algae to the rocky\nseabed and prevent them from being washed out to sea. Phaeophytes are usually found in\nareas of cold water.\n22.11.3 Rhodophytes\nRhodophytes are typically found in warmer seawater, and are more delicate and smaller\nthan brown algae (phaeophytes). Rhodophytes are also able to grow at deeper depths in\nthe ocean, since red algae absorb green, violet, and blue light, the wavelengths of which\npenetrate the deepest below the water surface. They also have mucilaginous material to\nresist drying.\n102"
  },
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    "page": 111,
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    "text": "Slime molds & Water molds\n22.11.4 Chryosophytes\nChryosophytes are the most abundant unicellular algae in the oceans. They are also one\nof the biggest components of plankton, a free-floating collection of microorganisms, eggs,\nand larvae. As photosynthetic organisms, they produce a significant amount of atmospheric\noxygen.\nThe reproduction cycle of chryosophytes is particularly interesting. Note that diatoms\nreproduce both asexually and sexually. Since diatoms have a rigid cell wall with an outer\nlayer of silica (found in sand and glass), the daughter cells produced by mitosis must fit\ninside the original cell wall. Therefore, each generation of diatoms is smaller than the one\nbefore. The reduction in size continues until the diatoms produce sexually, producing a\nzygote which eventually grows to the original size as it matures.\n22.11.5 Pyrrophytes\nPyrrophytes are unicellular, photosynthetic, and mostly aquatic. They have protective coats\ncomposed of stiff cellulose."
  },
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    "chunk_id": 214,
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    "page": 111,
    "chunk_index_in_page": 1,
    "text": "which eventually grows to the original size as it matures.\n22.11.5 Pyrrophytes\nPyrrophytes are unicellular, photosynthetic, and mostly aquatic. They have protective coats\ncomposed of stiff cellulose. They are more easily identifiable, due to the presence of two\nflagellae. The longer flagellae propels the dinoflagellate, while the second shorter, flatter\nflagellae functions as a rudder.\nSome species of pyrrophytes are zooxanthellae. Since they lack cellulose plates, they make\ntheir home in coral reefs and animals, such as sea anemones, and molluscs. In returning\nthe favour of sheltering them, dinoflagellates provide carbohydrates to their host through\nphotosynthesis. This is why there are nutrient-rich coral reefs in malnutritions water.\nA negative aspect of pyrrophytes is that under certain conditions, species of dinoflagellates\nreproduce rapidly to form a harmful algal bloom (HAB), known as a red tide if dinoflag-\nellates are the cause."
  },
  {
    "chunk_id": 215,
    "source_file": "GeneralBiology.pdf",
    "page": 111,
    "chunk_index_in_page": 2,
    "text": "gative aspect of pyrrophytes is that under certain conditions, species of dinoflagellates\nreproduce rapidly to form a harmful algal bloom (HAB), known as a red tide if dinoflag-\nellates are the cause. Such pyrrophytes can produce toxins which may injure or kill wildlife,\nand additionally any consumers of contaminated wildlife.\n22.11.6 Euglenophytes\nLike pyrrophytes, euglenophytes are small unicellular freshwater organisms with two flagella.\nThey are mainly autotrophic or heterotrophic, depending if they have a red, light-sensitive\nstructure called an eyespot.\n22.12 Slime molds & Water molds\nThere are two phyla of slime moulds and one phylum of water moulds.\n22.12.1 Oomycotes (Water moulds)\nOomycotes are filamentous organisms which resemble fungi, in that they live as saprotrophs.\nOomycotes differ from other moulds with the presence of spores and their sexual life cycle.\n103"
  },
  {
    "chunk_id": 216,
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    "page": 112,
    "chunk_index_in_page": 0,
    "text": "Classification of Living Things\n22.12.2 Myxomycotes (Plasmodial slime moulds)\nMyxomycotiesarevisibletothenakedeyeastinyslug-likeorganismswhichcreepoverdecayed\nand dead matter. This streaming blob containing many nuclei is called a plasmodium.\n22.12.3 Acrasiomycotes (Cellular slime moulds) and its reproductive\ncycle\nAcrasiomycotes exist as individual amoeboid cells with one nucleus each. When in un-\nfavourable conditions, each acrasiomycete cell gathers together to form a pseudoplasmod-\nium.\nReproductive Cycle:\n1. One acrasiomycete cell joins with others to form a pseudoplasmodium.\n2. The pseudoplasmodium shrinks and forms a smaller plasmodium.\n3. The plasmodium migrates to a suitable environment.\n4. The plasmodium develops a sporangia, where original parental nuclei has divided by\nmeiosis into haploid spores to be germinated.\n5. When favourable conditions arise, the spores germinate and are carried away by animals\nor the wind.\n6. Cycle repeats.\n22.13 Protists Practice Questions\n1."
  },
  {
    "chunk_id": 217,
    "source_file": "GeneralBiology.pdf",
    "page": 112,
    "chunk_index_in_page": 1,
    "text": "osis into haploid spores to be germinated.\n5. When favourable conditions arise, the spores germinate and are carried away by animals\nor the wind.\n6. Cycle repeats.\n22.13 Protists Practice Questions\n1. Which of the following adjectives describe the major food source of protozoa?\na) chemoautotrophic\nb) photoheterotrophic\nc) chemoheterotrophic\nd) heterotrophic\ne) A, C, D\nf) C, D\n2. The protozoan Giardia lamblia can inhabit a human body's intestinal tract and cause\ngastroenteritis.\na) Give the abbreviated binomial name of this protozoan.\nb) Would the relationship between this protozoan and human being be mutualistic, com-\nmensalistic, or parasitic?\n104"
  },
  {
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    "page": 113,
    "chunk_index_in_page": 0,
    "text": "Protists Practice Questions\n3. Found in many products, such as Petri dishes, agar is made from mucilagnious material\nin seaweed. Of the six phyla of algae, which phyllum/phyla would agar be made from?\n4. Which of the following adjectives describe the major food source of Euglenophytes without\nan eyespot?\na) photoautotrophic\nb) photoheterotrophic\nc) chemoautotrophic\nd) chemoheterotrophic\ne) B or C\nf) C or D\n5. Can coral reefs exist in nutrient-poor areas? Explain.\n105"
  },
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    "page": 115,
    "chunk_index_in_page": 0,
    "text": "23 Multicellular Photosynthetic\nAutotrophs\n23.1 Plants\n• Multicellular\n• Cellulose cell walls\n• Chlorophylls a and b\n• Develop from embryophyte\n• Alternation of generations\n• Major food source for terrestrial life\n• Atmospheric O2 and CO2 balance\n• Coal deposits\n• Intimate association with mycorrhizal fungi\n• >250,000 species (˜500,000?)\n• Taxonomy\n• State of flux\n• DNA sequencing\n• Developmental studies\n• Division (old literature) = phylum (new literature)\n• ˜12 phyla, 9 of which are vascular plants\n23.2 Plant phyla\nPhyla are 12 groupings\n23.3 Plant evolution\n• Evolved from green algae, likely related to charophytes\n• Evidence\n• DNA sequences\n• homologous chloroplasts: chlorophyll b and beta-carotene; thylakoids in grana;\n• Cellulose in both groups; also peroxisomes\n• Mitosis and cytokinesis similar\n• Sperm ultrastructure\n107"
  },
  {
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    "page": 116,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\n23.3.1 Terrestrial adaptations\n• Stomata: pores in leaves for exchange of gases; prevent desiccation\n• Secondary metabolites:\n• cuticle: waxy coating to prevent H2O loss\n• lignin: hardens wood\n• sporopollenin: resistant polymer; coats pollen\n• predator defenses\n• Embryonic development\n• gametangia in early plants\n• spores; seeds\n• Mycorrhizae\n• Water/food conducting systems\n23.4 Plant phylogeny\n23.5 Plant life cycles\n• Alternation of generations\n• Sporophyte\n• diploid\n• produces spores in sporangia\n• Gametophyte\n• develops from spore\n• haploid\n• produces gametes in gametangia\n• Haplodiplontic life cycle\n23.6 Moss life cycle\n23.7 Vascular plants\n• Most have roots\n• Aerial shoot systems\n• Vascular tissue\n• xylem: water, mineral transport\n• phloem: food transport\n• Lignin\n• Branched sporophyte is dominant stage\n• amplified production of spores\n• evolution of complex plant bodies\n• Dominated Carboniferous (360 my)\n108"
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    "page": 117,
    "chunk_index_in_page": 0,
    "text": "Vascular plant life cycles\n23.8 Vascular plant life cycles\n• Homosporous (single type of spore)\n• Heterosporous (two types of spore)\n23.9 Pterophyta (ferns)\n• Non-seed plant\n• Sporophyte conspicuous (vascular tissue)\n• Rhizome: ground stem, roots\n• Fronds: leaves\n• Sori: clusters of sporangia\n• Motile sperm require external water for fertilization\n• Originated in Devonian, 350 my\nTree fern Fern life cycle\n23.10 Non-seed plants, continued\n• Lycophyta: club mosses\n• E.g., Lycopodium (“ground pine”)\n• Many species became extinct 270 my, once dominant (coal formations)\n• Gametophyte non-photosynthetic, nourished by fungi\n• Arthrophyta: horsetails\n• Equisitum\n• Some fossil forms (300 my) were tree-size (coal)\n• Photosynthetic stems, no leaves\n• Silica deposits in epidermal cells\n23.11 Seed plants\n• 1st appeared in Devonian, 360 my\n• Seed develops from ovule, protects embryo\n• withstands drought\n• dispersal is enhanced\n• no immediate need for water for germination\n• Heterosporous"
  },
  {
    "chunk_id": 222,
    "source_file": "GeneralBiology.pdf",
    "page": 117,
    "chunk_index_in_page": 1,
    "text": "1 Seed plants\n• 1st appeared in Devonian, 360 my\n• Seed develops from ovule, protects embryo\n• withstands drought\n• dispersal is enhanced\n• no immediate need for water for germination\n• Heterosporous\n• male gametophyte: arise from microspores\n• female gametophyte: arise from megaspores in ovule in ovary\n• Two groups\n• gymnosperms\n• angiosperms\n109"
  },
  {
    "chunk_id": 223,
    "source_file": "GeneralBiology.pdf",
    "page": 118,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\nplant\n23.12 Sporophyte/gametophyte\n23.13 Megasporangium (nucellus)\n• Key to seed development\n• Nucellus: solid, fleshy, surrounded by integuments derived from sporophyte (seed coat)\n• Entire structure called ovule\n• Flower may have many ovules\n23.14 Pollen\n• Develop from microspores, become male gametophyte\n• Protected by sporopellenin\n• In most plants, sperm lack flagella (loss)\n• Many mechanisms to transport pollen\n• wind\n• insects, birds,\n23.15 Gymnosperms\n• “naked seed”\n• ovule not fully enclosed by sporophyte at time of pollination\n• Conifers, cycads, gnetophytes, Ginkgo\n• Small, inconspicuous plants to giants like sequoia\n• Conifers: to carry cones fv\n• male cones, Female conesvv\n• evergreen\n23.16 Pine life cycle\n23.17 Other Coniferophyta\n• Cycadophyta: cycads\n• tropical, subtropical\n• flagellated sperm\n• Gnetophyta\n• e.g., Ephedra, Mormon Tea\n• Ginkgophyta: Ginkgo\n110"
  },
  {
    "chunk_id": 224,
    "source_file": "GeneralBiology.pdf",
    "page": 119,
    "chunk_index_in_page": 0,
    "text": "Other gymnosperms\n• only one surviving species\n• diocious (separate % and &trees)\n23.18 Other gymnosperms\n23.19 Angiosperms\n• Flowering plants, Anthophyta\n• monocots- single seed leaf (grasses, lilies, etc.)\n• dicots- two seed leaves (roses, pulses, maples)\n• More specialized xylem (water transport)\n• vessel elements\n• fiber cells\n• Fossils date to 130 my\n• Animal (e.g., insect) coevolution\n23.19.1 Monocots vs dicots\n23.20 Earliest angiosperm\n• What is earliest angiosperm?\n• RecentanalysisofnucleotideandaminoacidsequencessuggeststhatAmborella,atropical\nplant found only on the island of New Caledonia, is closest relative to flowering plants\n23.21 Angiosperm flower\nInsert non-formatted text hereInsert non-formatted text here\n23.22 Angiosperm life cycle\nThis text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n23.23 Introduction\nAlthough you may not recognise fungi, they are just as prevalent as plants and animals."
  },
  {
    "chunk_id": 225,
    "source_file": "GeneralBiology.pdf",
    "page": 119,
    "chunk_index_in_page": 1,
    "text": "on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland\nState University.\n23.23 Introduction\nAlthough you may not recognise fungi, they are just as prevalent as plants and animals.\nTheir spores are in the air which we breathe, fungi allow us to make bread, and mushrooms\n(atypeoffungi)areeatenbyus. Afewtypesoffungiareunicellular. Forexample, yeastslive\nas individual oval or cylindrical cells. However, the majority of fungi live are multicellular.\nTheir bodies are composed of hyphae, a network of fine filaments. In a mushroom, the\n111"
  },
  {
    "chunk_id": 226,
    "source_file": "GeneralBiology.pdf",
    "page": 120,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\nhyphae are densely packed so it is difficult to see the individual structures when a mushroom\nis eaten. However, a mushroom is only a specialised reproductive part of the whole fungus.\nThe main part of the fungi is underground in a whole web of hyphae, called a mycelium.\nIn the mycelium, each fungal cell is separated from each other by a septum. Each fungal\ncell may have one or more nuclei and remains connected to the mycelium because the septa\nare porous, allowing cytoplasm to flow through the hyphae and fungal cell walls, made of a\nhard material called chitin. Some fungi do not have septa, and they appear to be large,\nbranching, multinucleate cells.\n23.24 Nutrition\nFungi are saprophytes. When they find a source of food (e.g. dead wood, orange peel) ,\nthey decompose it and digest it. The enzymes break down larger organic molecules in the\nsubstrate into smaller molecules. These smaller molecules diffuse into the fungus, where"
  },
  {
    "chunk_id": 227,
    "source_file": "GeneralBiology.pdf",
    "page": 120,
    "chunk_index_in_page": 1,
    "text": "d wood, orange peel) ,\nthey decompose it and digest it. The enzymes break down larger organic molecules in the\nsubstrate into smaller molecules. These smaller molecules diffuse into the fungus, where\nthey are used to allow growth and repair.\nFungi which feed on living cells are parasitic. For example, athlete's foot grows on the\nhuman foot. These kinds of fungi produce hyphae called haustoria, which can penetrate\nhost cells without immediately killing them.\nHowever, they are friendlier species of fungi. Many fungi live symbiotically with plants or\nanimals. For example, most trees have fungi living in close contact with their roots. In this\nrelationship, known as a mycorrhiza, there are many benefits:\n• Growing around the plant roots and often entering plant cells, the hyphae absorb minerals\nfrom the soil and release them in the roots. The fungi gets its source of food (organic\nnutrients) while delivering food to the plant."
  },
  {
    "chunk_id": 228,
    "source_file": "GeneralBiology.pdf",
    "page": 120,
    "chunk_index_in_page": 2,
    "text": "roots and often entering plant cells, the hyphae absorb minerals\nfrom the soil and release them in the roots. The fungi gets its source of food (organic\nnutrients) while delivering food to the plant.\n• The mycelium here would increase the surface area, thus the absorptive surface, of the\nplant roots.\n• The fungal cells help to maintain air and water flow in the soil around the roots.\n• The fungi may prevent other potentially pathogenic fungi to attack the tree.\n23.25 Fungal Reproduction\nFungi can reproduce in two ways. Firstly, they make asexually produce through frag-\nmentation. This occurs when pieces of hyphae are broken off, which then grow into new\nmycelia.\nThe second method is by spores. Spores are lightweight structures and windblown designed\nto be transported over long distances and by many mediums, such as on the bodies of insects\nand birds. They are additionally light enough to be blown away for hundreds of kilometers.\nSpores may be asexual and sexual."
  },
  {
    "chunk_id": 229,
    "source_file": "GeneralBiology.pdf",
    "page": 120,
    "chunk_index_in_page": 3,
    "text": "d over long distances and by many mediums, such as on the bodies of insects\nand birds. They are additionally light enough to be blown away for hundreds of kilometers.\nSpores may be asexual and sexual. Their sexual properties can be analysed to classify the\nfour phylla of fungi.\n112"
  },
  {
    "chunk_id": 230,
    "source_file": "GeneralBiology.pdf",
    "page": 121,
    "chunk_index_in_page": 0,
    "text": "Types of Fungi\n23.26 Types of Fungi\n23.26.1 Zygospore Fungi (Zygomycetes)\nThis phyllum includes bread moulds and other saprotrophs. Comparable to bacteria, this\nphyllum prefers asexual reproduction over sexual reproduction.\n1. Two haploid hyphae of opposite types, also known as mating strain + and mating\nstrain -, combine and fuse together.\n2. Plasmogamy, the union of the two parent hyphae, occurs and results in the creation\nof a heterokaryotic (n + n) zygosporangium or zygospore. Note that the zygospore is\nNOT diploid yet; the haploid nuclei are simply clumped together.\n3. Immediately, a thick wall develops around the zygospore to protect it from drying and\nother hazards. The zygospore becomes dormant.\n4. When conditions are favourable, the zygospore absorbs water and undergoes karyogamy\n(n + n = 2n), where the haploid nuclei contributed by the two parents fuse to produce\ndiploid zygosporangia.\n5. The now diploid zygosporangium then undergoes meiosis to form haploid sporangia.\n6."
  },
  {
    "chunk_id": 231,
    "source_file": "GeneralBiology.pdf",
    "page": 121,
    "chunk_index_in_page": 1,
    "text": "gamy\n(n + n = 2n), where the haploid nuclei contributed by the two parents fuse to produce\ndiploid zygosporangia.\n5. The now diploid zygosporangium then undergoes meiosis to form haploid sporangia.\n6. Through asexual reproduction of fungi (See above for more information), the spores from\nthe sporangia germinate and grow into new mycelia.\n7. Back to step #1.\n23.26.2 Club Fungi (Basidiomycetes)\nThis phyllum increases mushrooms and shelf fungi. In many ways, the reproduction stages\nof this phyllum is similar to that of zygomycetes.\n1. Two haploid hyphae of opposite types, also known as mating strain + and mating\nstrain -, combine and fuse together.\n2. Plasmogamy takes place, and a dikaryotic mycelium forms. The dikaryotic mycelium\ngrows faster then the haploid parental mycelia.\n3. Environmental factors cause the dikaryotic mycelium to form compact masses which de-\nvelop into basidiocarps, short-lived reproductive structures. An example is the mushroom.\n4."
  },
  {
    "chunk_id": 232,
    "source_file": "GeneralBiology.pdf",
    "page": 121,
    "chunk_index_in_page": 2,
    "text": "d parental mycelia.\n3. Environmental factors cause the dikaryotic mycelium to form compact masses which de-\nvelop into basidiocarps, short-lived reproductive structures. An example is the mushroom.\n4. The basidiocarp gills are lined with terminal dikaryotic cells called basidia, which then\nundergo karyogamy.\n5. The basidia are now diploid. They undergo meiosis to develop haploid basidiospores, a\nterm referring to a basidiomycete's spores.\n6. Stillremainingonthebasidiocarp,thehaploidbasidiosporeseject,fallfromthebasidiocarp,\nand are dispersed by the wind when mature.\n7. In a favourable environment, the basidiospores germinate and grow into short-lived\nhaploid mycelia.\n113"
  },
  {
    "chunk_id": 233,
    "source_file": "GeneralBiology.pdf",
    "page": 122,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\n8. Back to Step #1.\n23.27 Key Terms\nsynapomorphy\n23.28 Introduction\nWhat makes an animal an animal?\nIfanimalsareamonophyletictaxon, thenanimalsshouldbeabletobedefinedbysynapomor-\nphies, (shared, derived characteristics). Ideally, we would NOT definethis orany taxon using\nsymplesiomorphies (shared ancestral or primitive characteristics) or homoplastic characters\n(the independent evolution of similarity, or \"convergent evolution\"). See pages 654 - 656 and\nFig. 32.6 in your text to review these concepts. As you consider the characteristics listed\nbelow, ask yourself whether or not each is a synapomorphy.\n23.29 Characteristics of an Animal\n• There is no one universally accepted definition of an animal. The following treatment\nfollows your text, beginning on page 876.\n• Animals:\n• Are multicellular, heterotrophic eukaryotes ...\n• Lack the distinctive cell walls of plants & fungi\n• Share unique characteristics ..."
  },
  {
    "chunk_id": 234,
    "source_file": "GeneralBiology.pdf",
    "page": 122,
    "chunk_index_in_page": 1,
    "text": "treatment\nfollows your text, beginning on page 876.\n• Animals:\n• Are multicellular, heterotrophic eukaryotes ...\n• Lack the distinctive cell walls of plants & fungi\n• Share unique characteristics ...\n• Share certain reproductive characteristics ...\n• Other commonly used definitions ...\nAnimals are multicellular heterotrophic eukaryotes\n• Unfortunately, none of these traits is exclusive to animals:\n• Plants, fungi, and some algae are multicellular.\n• Many bacteria, protists, and all fungi are heterotrophic.\n• Everything other than bacteria and archaea are eukaryotic.\n• Moreover, all three of these characteristics also apply to fungi.\n• However, there is a difference here between animals and fungi. Animals generally\ntake in their food through ingestion, or eating and swallowing something. Fungi are\nabsorptive heterotrophs; they secrete their digestive enzymes onto their food, and then\nabsorb the resulting nutrients.\nAnimals share unique characteristics"
  },
  {
    "chunk_id": 235,
    "source_file": "GeneralBiology.pdf",
    "page": 122,
    "chunk_index_in_page": 2,
    "text": "eating and swallowing something. Fungi are\nabsorptive heterotrophs; they secrete their digestive enzymes onto their food, and then\nabsorb the resulting nutrients.\nAnimals share unique characteristics\n• Only animals have muscle tissue and nervous tissue.\n• Only animals have collagen, a structural protein\n• Only animals have the following types of intercellular junctions: (See pages 135 - 139,\nFigure 7.15 in your text for more information on these junctions.)\n114"
  },
  {
    "chunk_id": 236,
    "source_file": "GeneralBiology.pdf",
    "page": 123,
    "chunk_index_in_page": 0,
    "text": "Characteristics of an Animal\n• Tight junctions (sealing function)\n• Desmosomes (anchoring function)\n• Gap junctions (communication function)\nAnimals share certain reproductive characteristics\n• Most animals reproduce sexually, with the diploid stage dominating.\n• In most animals, a small, haploid, flagellated, motile sperm fertilizes a larger, haploid,\nnonmotile egg to form a diploid zygote.\n• Mitotic division of the zygote yields a blastula stage, followed by a gastrula stage. A\nsynapomorphy? This feature could be another \"unique characteristic\" shared by animals.\n• Development may be direct to adult form, or there may be a sexually immature stage\n(or stages) that are morphologically & ecologically distinct from the adult called a larva\n(plural: larvae).\nOther commonly used definitions or characterizations\n• It is surprisingly difficult to find two texts that agree on a precise definition of an animal.\nHere are a few perspectives from some other texts."
  },
  {
    "chunk_id": 237,
    "source_file": "GeneralBiology.pdf",
    "page": 123,
    "chunk_index_in_page": 1,
    "text": "her commonly used definitions or characterizations\n• It is surprisingly difficult to find two texts that agree on a precise definition of an animal.\nHere are a few perspectives from some other texts.\n• Animals are multicellular eukaryotes; they are chemosynthetic heterotrophs that ingest\ntheir food.\n• Animalsaremotile,thoughmanyaresecondarilysessile. Gametesusuallyareproduced\ninmulticellularsexorgans,andthezygotepassesthroughembryonicstagesthatinclude\na blastula.\n• Animals are organisms that are multicellular, with more than one type of cell. They\nare heterotrophic. They reproduce sexually (at least sometimes), with a zygote formed\nfrom two different haploid gametes. They go through a developmental stage called a\nblastula.\n• Animals are not photosynthetic, have no cell wall, and no hyphae or mycelia. (What\nwould a cladist think of this definition of the taxon Animalia?)\nWhat kinds of animals are there?\n• Kingdom Animalia generally is recognized to have approximately 30 phyla ..."
  },
  {
    "chunk_id": 238,
    "source_file": "GeneralBiology.pdf",
    "page": 123,
    "chunk_index_in_page": 2,
    "text": "yphae or mycelia. (What\nwould a cladist think of this definition of the taxon Animalia?)\nWhat kinds of animals are there?\n• Kingdom Animalia generally is recognized to have approximately 30 phyla ...\n• There is relatively little dispute over the number of phyla recognized; however, the\nphylogenetic relationships among the phyla are hotly debated.\n• Molecular techniques for assess similarity based on nucleotide sequences in nucleic\nacids are providing valuable new perspectives on this question.\n• Rememberthattwoanimalsindifferentphylagenerallyareconsideredtobemoredifferent\nfrom each other than are animals within one phylum (e.g., nematodes are more different\nfrom annelids than humans are from sharks).\nThis text is based on notes very generously donated by Ralph Gibson, Ph.D.1 of the Cleveland\nState University2.\n1 http://bgesweb.artscipub.csuohio.edu/faculty/gibson.htm\n2 http://www.csuohio.edu\n115"
  },
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    "page": 124,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\n23.30 Introduction to animal phyla\nThere currently are almost 40 recognized phyla.\nPhylum — Number of Species — Common Name\n• Placozoa3 — 1\n• Monoblastozoa4 — 1\n• Rhombozoa5 — 50\n• Orthonectida6 — 50\n• Porifera7 — 9,000 — sponges (figures)\n• Cnidaria8 — 9,000 — corals (figures)\n• Ctenophora9 — 100 — comb jellies\n• Platyhelminthes10 — 20,000 — flatworms (figures)\n• Nemertea11 — 900 — ribbon worms (figures)\n• Rotifera12 — 1,800 — rotifers (figures)\n• Gastrotricha13 — 450 — gastrotrichs\n• Kinorhyncha — 150 — kinorhynchids\n• Nematoda — 12,000 — roundworms (figures)\n• Nematomorpha — 230 — horsehair worms\n• Priapula — 15\n• Acanthocephala — 700 — (figures)\n• Entoprocta — 150\n• Gnathostomulida — 80\n• Loricifera — 35\n• Annelida — 15,000 — segmented worms (figures)\n• Sipuncula — 250 — peanut worms (figures)\n• Echiura — 135\n• Pogonophora — 145 — beard worms\n• Vestimentifera — 8 — beard worms\n• Arthropoda — 957,000 — arthropods (figures)\n• Onychophora — 80"
  },
  {
    "chunk_id": 240,
    "source_file": "GeneralBiology.pdf",
    "page": 124,
    "chunk_index_in_page": 1,
    "text": "gures)\n• Sipuncula — 250 — peanut worms (figures)\n• Echiura — 135\n• Pogonophora — 145 — beard worms\n• Vestimentifera — 8 — beard worms\n• Arthropoda — 957,000 — arthropods (figures)\n• Onychophora — 80\n• Tardigrada — 400 — water bears\n• Pentastomida — 95 — tongue worms\n• Mollusca — 100,000 — molluscs (figures)\n• Phoronida — 15\n• Ectoprocta — 4,500 — sessile zooids\n• Brachiopoda — 335 — lampshells\n3 http://en.wikibooks.org/wiki/Placozoa\n4 http://en.wikibooks.org/wiki/Monoblastozoa\n5 http://en.wikibooks.org/wiki/Rhombozoa\n6 http://en.wikibooks.org/wiki/Orthonectida\n7 http://en.wikibooks.org/wiki/Porifera\n8 http://en.wikibooks.org/wiki/Cnidaria\n9 http://en.wikibooks.org/wiki/Ctenophora\n10 http://en.wikibooks.org/wiki/Platyhelminthes\n11 http://en.wikibooks.org/wiki/Nemertea\n12 http://en.wikibooks.org/wiki/Rotifera\n13 http://en.wikibooks.org/wiki/Gastrotricha\n116"
  },
  {
    "chunk_id": 241,
    "source_file": "GeneralBiology.pdf",
    "page": 125,
    "chunk_index_in_page": 0,
    "text": "Phylum Porifera\n• Echinodermata — 7000 — echinoderms (figures)\n• Chaetognatha — 100 — arrow worms (figures)\n• Hemichordata — 85 — acorn worms\n• Chordata — 50,000 — chordates (figures)\n23.31 Phylum Porifera\nFigure 6 Sponges\nName means \"pore-bearing\".\nThis phylum consists of the sponges. The number of species is estimated to be between\n5,000 and 10,000. All are aquatic and almost all are marine.\nAnimals in this phyla have no true tissues, which means, for example, that they have no\nnervous system or sense organs. Although sponges are multicellular, they are described as\nbeing essentially at a cellular level of organization. They are sessile as adults, but have a\nfree swimming larva.\nTheir bodies are porous. They are filter feeders; water flows in through many small openings,\nand out through fewer, large openings. They have inner and outer cell layers, and a variable\nmiddle layer. The middle layer often is gelatinous with spiny skeletal elements (called"
  },
  {
    "chunk_id": 242,
    "source_file": "GeneralBiology.pdf",
    "page": 125,
    "chunk_index_in_page": 1,
    "text": "ny small openings,\nand out through fewer, large openings. They have inner and outer cell layers, and a variable\nmiddle layer. The middle layer often is gelatinous with spiny skeletal elements (called\nspicules) of silica or calcium carbonate, and fibres made of spongin (a form of collagen).\n117"
  },
  {
    "chunk_id": 243,
    "source_file": "GeneralBiology.pdf",
    "page": 126,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\nChoanocytes are flagellated cells lining the inside of the body that generate a current, and\ntrap and phagocytize food particles.\nTheir cells remain totipotent, or developmentally flexible: they can become any type of\ncell at any point in the sponge's development. This allows for the great regenerative power\nsponges have.\nSponges are an ancient group, with fossils from the early Cambrian (ca. 540 mya) and\npossibly from the Precambrian. Sponges often are abundant in reef ecosystems. They\nsomehow are protected from predators (spicules? bad taste?).\nMany organisms are commensals of sponges, living inside them. Some sponges harbor\nendosymbiotic cyanobacteria or algae (dinoflagellates, a.k.a. \"zooxanthellae\").\n23.32 Phylum Cnidaria\nSee text pages 886 - 889.\nName comes from the Greek knide- meaning \"nettle\".\nThis phylum They have one opening, which serves as both mouth and anus. The body wall"
  },
  {
    "chunk_id": 244,
    "source_file": "GeneralBiology.pdf",
    "page": 126,
    "chunk_index_in_page": 1,
    "text": "oxanthellae\").\n23.32 Phylum Cnidaria\nSee text pages 886 - 889.\nName comes from the Greek knide- meaning \"nettle\".\nThis phylum They have one opening, which serves as both mouth and anus. The body wall\nhas an outer ectoderm, an inner endoderm, and a variable undifferentiated middle layer\ncalled mesoglea or mesenchyme that may be jelly-like. The mesoglea is NOT considered\nto be true mesoderm and so the Cnidaria are described as diploblastic. Tentacles usually\nextend from the body wall around the mouth/anus.\n118"
  },
  {
    "chunk_id": 245,
    "source_file": "GeneralBiology.pdf",
    "page": 127,
    "chunk_index_in_page": 0,
    "text": "Phylum Cnidaria\nFigure 7 Jellyfish Development\nThere are two basic body plans: the polyp14 and the medusa15. The polyp is sessile and\nattaches to substrate by the aboral end (i.e., the end away from the mouth). The medusa\n(\"jellyfish\") is a floating form, and looks like an upside-down version of the polyp. Some\ncnidarians only have the polyp stage, some have only the medusa stage, and others have\nboth.\n14 http://en.wikipedia.org/wiki/polyp\n15 http://en.wikipedia.org/wiki/Medusa%20%28biology%29\n119"
  },
  {
    "chunk_id": 246,
    "source_file": "GeneralBiology.pdf",
    "page": 128,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\nThe typical life cycle of a cnidarian involves what is called \"alternation of generations\": an\nalternation between an asexual polyp stage and a sexual medusa stage.\nThe tentacles are armed with cnidae (or nematocysts), small intracellular \"harpoons\" that\nfunction in defense and prey capture. When fired, the cnidae deliver a powerful toxin that\nin some cases is dangerous to humans. The phylum is named after the cnidae.\nCnidarians have no head, no centralized nervous system, and no specialized organs for gas\nexchange, excretion, or circulation. They do have a \"nerve net.\"\nMany cnidarians have intracellular algae living within them in a mutualistic symbiotic\nrelationship (Dinoflagellates = zooxanthellae). This combination is responsible for much of\nthe primary productivity of coral reefs.\nThere are three main classes in the phylum\n• ClassHydrozoa16 (hydrasandPortugeseman-of-wararewell-knownbutatypicalexamples\nof this Class)"
  },
  {
    "chunk_id": 247,
    "source_file": "GeneralBiology.pdf",
    "page": 128,
    "chunk_index_in_page": 1,
    "text": "ponsible for much of\nthe primary productivity of coral reefs.\nThere are three main classes in the phylum\n• ClassHydrozoa16 (hydrasandPortugeseman-of-wararewell-knownbutatypicalexamples\nof this Class)\n• Class Scyphozoa17 (jellyfish)\n• The medusa stage is dominant and the polyp stage often is reduced.\n• Class Anthozoa18 (sea anemones, most corals)\n• No medusa (jellyfish) stage, so sexual reproduction occurs in the polyp stage in this\ngroup. The polyps also can reproduce asexually, which is how individual \"corals\" grow.\n23.33 Phylum Platyhelminthes\nSee text pages 890 - 893.\nName means \"flat worm\"\nMost members of this phylum are parasitic (flukes and tapeworms), but some are free living\n(e.g., planaria). There are about 20,000 species.\nThey are dorsoventrally compressed (i.e., \"flat\").\nAnimals in this phylum are acoelomate, triploblastic, bilaterally symmetrical, and unseg-\nmented. Platyhelminths have a simple anterior \"brain\" and a simple ladder-like nervous\nsystem."
  },
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    "page": 128,
    "chunk_index_in_page": 2,
    "text": "(i.e., \"flat\").\nAnimals in this phylum are acoelomate, triploblastic, bilaterally symmetrical, and unseg-\nmented. Platyhelminths have a simple anterior \"brain\" and a simple ladder-like nervous\nsystem. Their gut has only one opening. Flatworms have NO circulatory or gas exchange\nsystems. Theydohavesimpleexcretory/osmoregulatorystructures(protonephridiaor\"flame\ncells\").\nPlatyhelminths are hermaphroditic, and the parasitic species often have VERY complex\nreproductive (life) cycles.\nThere are four main classes of platyhelminths:\n• Class Turbellaria19 (mostly free living flatworms, e.g., planaria)\n16 http://en.wikipedia.org/wiki/Hydrozoa\n17 http://en.wikipedia.org/wiki/Scyphozoa\n18 http://en.wikipedia.org/wiki/Anthozoa\n19 http://en.wikipedia.org/wiki/Turbellaria\n120"
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    "page": 129,
    "chunk_index_in_page": 0,
    "text": "Phylum Rotifera\n• Class Monogenea20 (parasitic flukes)\n• Class Trematoda21 (parasitic flukes, e.g., liver fluke and the human blood fluke, Schisto-\nsoma)\n• Class Cestoda22 (tapeworms)\n• Cestodes are endoparasitic in the gut of vertebrates. They do not have a mouth or\ndigestive system.\n23.34 Phylum Rotifera\nSee text page 900\nThe Rotifers. The name means \"wheel bearing,\" a reference to the corona, a feeding structure\n(see below).\nThey are triploblastic, bilaterally symmetrical, and unsegmented. They are considered\npseudocoelomates.\nMost less than 2 mm, some as large as 2 - 3 mm.\nRotifers have a three part body: head, trunk foot. The head has a ciliary organ called the\ncorona that, when beating, looks like wheels turning, hence the name of the phylum. The\ncorona is a feeding structure that surrounds the animal's jaws. The gut is complete (i.e.,\nmouth & anus), and regionally specialized. They have protonephridia but no specialized\ncirculatory or gas-exchange structures."
  },
  {
    "chunk_id": 250,
    "source_file": "GeneralBiology.pdf",
    "page": 129,
    "chunk_index_in_page": 1,
    "text": "g structure that surrounds the animal's jaws. The gut is complete (i.e.,\nmouth & anus), and regionally specialized. They have protonephridia but no specialized\ncirculatory or gas-exchange structures.\nMost live in fresh water, a very few are marine or live in damp terrestrial habitats. They\ntypically are very abundant. There are about 2,000 species.\nParthenogenesis, where females produce more females from unfertilized but diploid eggs, is\ncommon. Males may be absent (as in bdelloid rotifers) or reduced. When males are present,\nsexual and asexual life cycles alternate. Males develop from unfertilized haploid eggs and\nare haploid. Males produce sperm by mitosis which can fertilize haploid eggs, yielding a\ndiploid zygote that develops into a diploid female. Sexual reproduction occurs primarily\nwhen living conditions are unfavorable.\nMoststructuresinrotifersaresyncytial(\"amulitnucleatemassofprotoplasmnotdividedinto"
  },
  {
    "chunk_id": 251,
    "source_file": "GeneralBiology.pdf",
    "page": 129,
    "chunk_index_in_page": 2,
    "text": "te that develops into a diploid female. Sexual reproduction occurs primarily\nwhen living conditions are unfavorable.\nMoststructuresinrotifersaresyncytial(\"amulitnucleatemassofprotoplasmnotdividedinto\nseparate cells,\" or \"a multinucleated cell\") and show eutely (here, \"constant or near-constant\nnumber of nuclei\").\n23.35 Phylum Nematoda\nSee text pages 894 - 895.\nName from the Greek for \"thread\".\n20 http://en.wikipedia.org/wiki/Monogenea\n21 http://en.wikipedia.org/wiki/Trematoda\n22 http://en.wikipedia.org/wiki/Cestoda\n121"
  },
  {
    "chunk_id": 252,
    "source_file": "GeneralBiology.pdf",
    "page": 130,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\nThis phylum consists of the round worms. There are about 12,000 named species but the\ntrue number probably is 10 - 100 times this!\nThese animals are triploblastic, bilaterally symmetrical, unsegmented pseudocoelomates.\nThey are vermiform, or wormlike.\nIn cross-section, they are round, and covered by a layered cuticle (remember this cuticle !!).\nProbably due to this cuticle, juveniles in this phylum grow by molting. The gut is complete.\nThey have a unique excretory system but they lack special circulatory or gas-exchange\nstructures. The body has only longitudinal muscle fibers. The sexes are separate.\nNematodes can be incredibly common, widespread, and of great medical and economic\nimportance. They are parasites of humans and our crops. They can live pretty much\nanywhere.\nIn one rotting apple, there can be up to 90,000 nematodes, and in one tablespoon of coastal\nmud, there can be 236 species of nematodes!"
  },
  {
    "chunk_id": 253,
    "source_file": "GeneralBiology.pdf",
    "page": 130,
    "chunk_index_in_page": 1,
    "text": "es of humans and our crops. They can live pretty much\nanywhere.\nIn one rotting apple, there can be up to 90,000 nematodes, and in one tablespoon of coastal\nmud, there can be 236 species of nematodes!\nNematodes can be free living or important parasites of our crops, or of humans and other\nanimals. They have become very important in development studies, especially the species\nCaenorhabditis elegans, presumably due to its small size and constancy of cell number\n(eutely - 959 cells in C. elegans).\n23.36 Phylum Annelida\nSee text pages 906 - 909.\nName means \"ringed\", from the Greek annulatus.\nThis phylum consists of earthworms, leeches, and various marine worms given many different\nnames (e.g., sand worms, tube worms). There are about 12,000 - 15,000 species.\nAnimals in this phylum are triploblastic, bilaterally symmetrical, segmented coelomates.\nDevelopment is typically protostomous. They have a complete circulatory system, and\na well-developed nervous system."
  },
  {
    "chunk_id": 254,
    "source_file": "GeneralBiology.pdf",
    "page": 130,
    "chunk_index_in_page": 2,
    "text": "ls in this phylum are triploblastic, bilaterally symmetrical, segmented coelomates.\nDevelopment is typically protostomous. They have a complete circulatory system, and\na well-developed nervous system. Typically, each segment has paired epidermal \"bristles\"\n(setae or chaetae).\nMost are marine but they are successful occupants of almost anywhere sufficient water is\navailable. They can be free living, parasitic, mutualistic, or commensalistic.\nMajor advances of this phylum include the true coelom, segmentation, both longitundinal\nand circular muscles, a closed circulatory system and, for most, a more advanced excretory\nsystem (metanephridia).\nThere are three main classes of Annelids\n• Class Oligochaeta (earthworms)\n• Class Polychaeta (marine worms)\n• Class Hirudinea (leeches)\n122"
  },
  {
    "chunk_id": 255,
    "source_file": "GeneralBiology.pdf",
    "page": 131,
    "chunk_index_in_page": 0,
    "text": "Phylum Arthropoda\n23.37 Phylum Arthropoda\nFigure 8 Arthropods\nName means \"jointed feet\".\nThis phylum consists of spiders, ticks, mites, insects, lobsters, crabs, and shrimp, and is the\nlargest of all the phyla. So far, over 1 million species have been named, and it is likely that\nthe true number out there is 10 - 100 times greater.\nThis phylum also includes the extinct trilobites, which were prevalent in the Paleozoic era.\nBecause of their exoskeletons, these animals fossilized well and over 4000 species have been\nnamed.\nThese animals are triploblastic, bilaterally symmetrical, segmented, protostome coelomates.\nThe coelom is generally reduced to portions of the reproductive and excretory systems. They\nhave an open circulatory system.\nThemostnotableadvancementofthisphylumisarigidexoskeleton. Ithasmajorimplications\nin these organisms' locomotion, flexibility, circulatory systems, gas exchange systems, and\ngrowth."
  },
  {
    "chunk_id": 256,
    "source_file": "GeneralBiology.pdf",
    "page": 131,
    "chunk_index_in_page": 1,
    "text": "circulatory system.\nThemostnotableadvancementofthisphylumisarigidexoskeleton. Ithasmajorimplications\nin these organisms' locomotion, flexibility, circulatory systems, gas exchange systems, and\ngrowth. It also was partially responsible for the ability of the arthropods to move on to land.\nThere are several major groupings of arthropods:\nMajor subgroups include:\n• The chelicerates (eurytperids, horseshoe crabs, scorpions, spiders, ticks) have clawlike\nfeeding appendages. They lack antennae and usually have simple eyes.\n• The Trilobites...they get their own grouping\n123"
  },
  {
    "chunk_id": 257,
    "source_file": "GeneralBiology.pdf",
    "page": 132,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\n• The uniramians (centipedes, millipedes, insects) have one pair of antennae and un-\nbranched (uniramous) appendages.\n• The crustaceans (crabs, shrimp, lobsters, barnacles and many others) have two pairs of\nantennae and branched (biramous) appendages.\nMajor Classes Include\n• Class Arachnida (mites, scorpions, spiders, ticks)\n• Class Diplopoda (millipedes)\n• Class Chilopoda (centipedes)\n• Class Insecta (insects)\n• Class Crustacea (crabs, crayfish, lobsters, shrimp)\n23.38 Phylum Mollusca\nSee text pages 900 - 905.\nName means \"soft\".\nThis phylum consists of snails, slugs, bivalves, chitons, squids, octopus, and many others.\nAbout 110,000 species\nAll molluscs have a similar body plan:\n• A muscular foot, usually used for movement.\n• A visceral mass, containing most of the internal organs.\n• A mantle, a fold of tissue that drapes over the visceral mass and secretes the shell, if\npresent.\n• Most have a radula, or a rasping organ to scrape food."
  },
  {
    "chunk_id": 258,
    "source_file": "GeneralBiology.pdf",
    "page": 132,
    "chunk_index_in_page": 1,
    "text": "s, containing most of the internal organs.\n• A mantle, a fold of tissue that drapes over the visceral mass and secretes the shell, if\npresent.\n• Most have a radula, or a rasping organ to scrape food.\nMolluscs are bilaterally symmetrical, or secondarily asymmetrical. They are coelomates, but\nthe coelom generally has been greatly reduced; the main body cavity is a hemocoel. Devel-\nopment is typically protostomous. The gut is complete with marked regional specialization.\nLarge, complex, metanephridia (excretion).\nMany molluscan life cycles include a trochophore larva. This stage also is characteristic of\nannelids.\nThere are several major classes of molluscs:\n• Class Polyplacophora (chitons)\n• Class Gastropoda (snails, slugs, nudibranchs)\n• Class Bivalvia (clams, mussels, scallops, oysters)\n• Class Cephalopoda (squids, octopuses, chambered nautiluses)\n23.39 Phylum Echinodermata\nName means \"spiny skin\"\nThis phylum consists of sea stars, brittle stars, sea urchins, and sea cucumbers.\n124"
  },
  {
    "chunk_id": 259,
    "source_file": "GeneralBiology.pdf",
    "page": 133,
    "chunk_index_in_page": 0,
    "text": "Phylum Chordata\nEchinoderms are mostly sessile or very slow moving animals.\nAs adults, they are radially symmetrical, but in the larval stage, they are bilaterally\nsymmetrical. They are considered deuterostomes.\nEchinoderms are unique in that they have a water vascular system composed of a system\nof fluid-filled canals. These canals branch into the tube feet, which function in feeding,\nlocomotion, and gas exchange.\nThere are six major classes of echinoderms:\n• Class Asteroidea (sea stars)\n• Class Ophiuroidea (brittle stars)\n• Class Echinoidea (sea urchins, sand dollars)\n• Class Crinoidea (sea lilies)\n• Class Holothuroidea (sea cucumbers)\n23.40 Phylum Chordata\nName means \"the chordates\", i.e., these animals have a notochord at some stage in their\nlifecycle.\nThis phylum consists of tunicates, lancelets, and the vertebrates.\nThere are four major features that characterize the phylum Chordata.\n• A notochord, or a longitudinal, flexible rod between the digestive tube and the nerve\ncord."
  },
  {
    "chunk_id": 260,
    "source_file": "GeneralBiology.pdf",
    "page": 133,
    "chunk_index_in_page": 1,
    "text": "ates, lancelets, and the vertebrates.\nThere are four major features that characterize the phylum Chordata.\n• A notochord, or a longitudinal, flexible rod between the digestive tube and the nerve\ncord. In most vertebrates, it is replaced developmentally by the vertebral column. This\nis the structure for which the phylum is named.\n• A dorsal hollow nerve cord which develops from a plate of ectoderm that rolls into a tube\nlocated dorsal to the notochord. Other animal phyla have solid nerve cords ventrally\nlocated. A chordate nerve cord splits into the central nervous system: the brain and\nspinal cord.\n• Pharyngeal slits, which allow water that enters through the mouth to exit without\ncontinuing through the entire digestive tract. In many of the invertebrate chordates,\nthese function as suspension feeding devices; in vertebrates, they have been modified for\ngas exchange, jaw support, hearing, and other functions.\n• A muscular, postanal tail which extends posterior to the anus."
  },
  {
    "chunk_id": 261,
    "source_file": "GeneralBiology.pdf",
    "page": 133,
    "chunk_index_in_page": 2,
    "text": "ion as suspension feeding devices; in vertebrates, they have been modified for\ngas exchange, jaw support, hearing, and other functions.\n• A muscular, postanal tail which extends posterior to the anus. The digestive tract of\nmost nonchordates extends the length of the body. In chordates, the tail has skeletal\nelements and musculature, and can provide most of the propulsion in aquatic species.\nChordates have a segmented body plan, at least in development. This segmentation evolved\nindependently from the segmentation of annelids.\nThree subphyla make up the phylum Chordata:\n• Subphylum Urochordata (tunicates): the adults are enclosed in a tunic made of a carbo-\nhydrate much like cellulose. They squirt water out of an excurrent siphon. Urochordates\nare characterized by errant (mobile and active) larvae and sessile adults. All are filter\nfeeders. The only \"chordate\" characteristics retained in adult life are the pharyngeal slits.\n125"
  },
  {
    "chunk_id": 262,
    "source_file": "GeneralBiology.pdf",
    "page": 134,
    "chunk_index_in_page": 0,
    "text": "Multicellular Photosynthetic Autotrophs\nLarval urochordates look more like adult cephlochordates & adult vertebrates than adult\nurochordates.\n• Subphylum Cephalochordata: Cephalochordates are known as lancelets because of their\nblade-like shape; they are also known as amphioxus. They are marine animals and usually\nlive on the bottom, but can swim.\n• Subphylum Vertebrata (vertebrates) ...\nFormally, the phyla Urochordata and Cephalochordata are considered invertebrates.\n23.40.1 Subphylum Vertebrata\nVertebrata refers to the presence of vertebrae and a vertebral column.\nThis subphylum includes most of the animals with which most people are familiar.\nVertebrates show extreme cephalization.\nThe notochord generally is replaced by the cranium & vertebral column in adults.\nNeural Crest Cells\nLater in development, these give rise to many cells of the body, including some cartilage\ncells, pigment cells, neurons & glial cells of the peripheral nervous systems, much of the"
  },
  {
    "chunk_id": 263,
    "source_file": "GeneralBiology.pdf",
    "page": 134,
    "chunk_index_in_page": 1,
    "text": "Neural Crest Cells\nLater in development, these give rise to many cells of the body, including some cartilage\ncells, pigment cells, neurons & glial cells of the peripheral nervous systems, much of the\ncranium, and some of the cells of the endocrine system.\nSome scientists would like to classify the neural crest as the fourth germ layer.\nNeural crest cells come from the dorsal edge of the neural plate, thus ectoderm.\n126"
  },
  {
    "chunk_id": 264,
    "source_file": "GeneralBiology.pdf",
    "page": 135,
    "chunk_index_in_page": 0,
    "text": "24 Chordates\nThe phylum Chordata includes three subphyla. These include vertebrates and invertebrate\nchordates.\n24.1 Characteristics\nNotochord: the rod-shaped supporting axis found in the dorsal part of the embryos of all\nchordates, including vertebrates\nFlexible, non-collapsible rod dorsal to the gut/coelom and below the nervous system,\nhydrostatic, fluid wrapped in tough connective tissue. As bone does not compact, muscles\ntensed on one side result in movement instead of shortening the animal. This allows much\nbetter locomotion than do cilia for larger animals in water, a crucial victory for later success.\nPharyngeal slits: Slits in the pharynx originally used to gather food, water enters the mouth,\npasses through pharynx and out gill-like slits, passing through a cavity called an antrium\nand then outside. In humans, present only in embryo.\nDorsal nerve cord: A neural tube dorsal to the notochord"
  },
  {
    "chunk_id": 265,
    "source_file": "GeneralBiology.pdf",
    "page": 135,
    "chunk_index_in_page": 1,
    "text": "asses through pharynx and out gill-like slits, passing through a cavity called an antrium\nand then outside. In humans, present only in embryo.\nDorsal nerve cord: A neural tube dorsal to the notochord\nPostanal tail: Elongation of the body and notochord, nerve cord and muscles past anus into\ntail, early locomotive function led to success.\nNon-synapomorphic characteristics (not limited to chordates):\n• bisymmetrical (bilateral symmetry)\n• segmented muscles and bones\n24.2 Subphylum Urochordata\nThe tunicates are located in this subphylum. Along with the subphylum Cephalochordata,\nthese two subphyla make up the invertebrate chordates. Only the tunicate larvae have\nnotochords, nerve cords, and postanal tails. Most adult tunicates are sessile, filter-feeders\nwhich retain their pharyngeal slits. Adult tunicates also develop a sac, called a tunic,\nwhich gives tunicates their name. Cilia beating within the turnicate cause water to enter\nthe incurrent siphon."
  },
  {
    "chunk_id": 266,
    "source_file": "GeneralBiology.pdf",
    "page": 135,
    "chunk_index_in_page": 2,
    "text": "which retain their pharyngeal slits. Adult tunicates also develop a sac, called a tunic,\nwhich gives tunicates their name. Cilia beating within the turnicate cause water to enter\nthe incurrent siphon. The water enters the body, passes through the pharyngeal slits,\nand leaves the body through the excurrent siphon. Undigested food is removed through\nthe anus. Tunicates are hemaphrodites and can reproduce asexually through budding.In\nurochordates notochord is confined to larval tail.These lack cranium. These have an open\ntype of circulatory system.Excretion is by neural gland,nephrocytes.\n127"
  },
  {
    "chunk_id": 267,
    "source_file": "GeneralBiology.pdf",
    "page": 136,
    "chunk_index_in_page": 0,
    "text": "Chordates\n24.3 Subphylum Cephalochordata\nThe lancelets are located in this subphylum. Along with the subphylum Urochordata, these\ntwo subphyla make up the invertebrate chordates. Lancelets receive their name from their\nbladelike shape. They resemble fish but they are actually scaleless chordates only a few\ncentimeters long. They spend most of their time buried in the sand with their mouths\nprotruding. Fossils of lancelets have been found to be over 550 million years old.\nDropped out sessile stage, what was the larval stage is now sexually reproductive. Includes\nBranchiostoma (“amphioxus”).\n24.4 Subphylum Vertebrata\n(Vertebra from Latin vertere, to turn). Characterized by separate bones or cartilage blocks\nfirmly joined as a backbone. The backbone supports and protects a dorsal nerve cord.\nVertebrates have tissues which are organized into organs which in turn are organized into\norgan systems."
  },
  {
    "chunk_id": 268,
    "source_file": "GeneralBiology.pdf",
    "page": 136,
    "chunk_index_in_page": 1,
    "text": "ge blocks\nfirmly joined as a backbone. The backbone supports and protects a dorsal nerve cord.\nVertebrates have tissues which are organized into organs which in turn are organized into\norgan systems.\nAll vertebrates share the following characteristics: - segmentation - a true coelom - bilateral\nsymmetry-cephalization-abackbone-abonyskull-aclosedcirculatorysystem-chambered\nheart - two pairs of jointed appendages - tissues organized into organs\nVertebrate Organ Systems: - Nervous System - Circulatory System - Digestive System -\nRespiratory System - Reproductive System - Excretory System\n• Vertebral column: Not present in higher vertebrate adults. (In humans, the gel-like,\nspongy core of the vertebral column is the only remainder. Ruptured or herniated disc is\nan injury to this.)\n• Cranium: Composite structure of bone/cartilage. Two functions: 1. Supports sensory\norgans of head and 2. Encloses or partially encloses the brain."
  },
  {
    "chunk_id": 269,
    "source_file": "GeneralBiology.pdf",
    "page": 136,
    "chunk_index_in_page": 2,
    "text": "Ruptured or herniated disc is\nan injury to this.)\n• Cranium: Composite structure of bone/cartilage. Two functions: 1. Supports sensory\norgans of head and 2. Encloses or partially encloses the brain.\nWhat evolutionary relationship could we imagine between sessile echinoderms and the higher\nchordate animals?\nPaedomorphic (child-form) hypothesis: basically, evolution of sexual reproduction in what\nhad previously been a larval life stage, or the retention of at least one juvenile characteristic\nintotheadult(adult=sexuallyreproducing)stage. Somescientistsbelievethatthisoccurred\nin a proto-chordate animal lineage. Maybe chordates (and vertebrates) arose from sessile\n(attached) ancestors. Selection in these proto-chordates maybe began to favor more time in\nthe larval stage, as feeding was more successful or mortality lower in this stage. As larvae\ngot bigger physics shows that the cilia become less efficient for locomotion, favoring the\nundulating motion allowed by a notochord."
  },
  {
    "chunk_id": 270,
    "source_file": "GeneralBiology.pdf",
    "page": 136,
    "chunk_index_in_page": 3,
    "text": "ng was more successful or mortality lower in this stage. As larvae\ngot bigger physics shows that the cilia become less efficient for locomotion, favoring the\nundulating motion allowed by a notochord.\nIs this hypothesis crazy? A similar example of this today is Epemeroptera, the mayfly, which\nhas almost abandoned its adult stage. Its one-year lifespan is mostly larval with just a brief\nday of reproduce-and-die as an adult, which doesn’t even have usable mouthparts.\nTunicate (sea squirt) larva has all four chordate characteristics, although adult sessile\n(“attached”).\n128"
  },
  {
    "chunk_id": 271,
    "source_file": "GeneralBiology.pdf",
    "page": 137,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\n24.4.1 Class Agnatha\n\"jawless fish\"\n• Ostracoderms: extinct Agnathans which had primitive fins and massive plates of bony\ntissue on their body.\n• Cyclostomes: \"circle mouth\" - a group of Agnathans which is still alive in the form of\nlampreys and hagfish.\nAppeared approximately 500 million years ago and dominated the oceans for about 100\nmillion years. The first group of fish to appear. They had neither jaws, paired fins, nor\nscales, but they were the first organisms with a backbone.\nClass Acanthodia\n\"spiny fish\" Appeared about 430 million years ago. An extinct class of fish that developed\njaws with bony edges. They had internal skeletons made of cartilage and some bone.\nClass Placodermi\nAppeared about 410 million years ago, dominated the sea for about 50 million years. An\nextinct class of fish with massive heads.\n24.4.2 Class Chondrichthyes\n\"cartilaginous fish\" Appeared about 400 million years ago with bony fish. Includes sharks,\nskates and rays, and chimaeras."
  },
  {
    "chunk_id": 272,
    "source_file": "GeneralBiology.pdf",
    "page": 137,
    "chunk_index_in_page": 1,
    "text": "ars. An\nextinct class of fish with massive heads.\n24.4.2 Class Chondrichthyes\n\"cartilaginous fish\" Appeared about 400 million years ago with bony fish. Includes sharks,\nskates and rays, and chimaeras. Their skeletons are made of cartilage strengthened by the\nmineral calcium carbonate.\nThe main characteristics and distinguishing features of this class: - gills - single-loop blood\ncirculation - vertebral column - presence of placoid scales on their bodies - internal skeleton\nof cartilage - paired, fleshy pectoral and pelvic fins - asymmetrical tail fin prevents sinking -\nfatty liver provides neutral buoyancy - visceral clefts present as separate and distinct gills -\nno external ear - oviparous - internal fertilization - ectoderms - cold blooded\n24.4.3 Class Osteichthyes\n\"bony fish\" Appeared about 400 million years ago with cartilaginous fish. Includes about\n95% of today's fish species.\nSubclass Sarcopterygii\nfleshy-finned fishes. Fins have bones and muscles, homologous to our limbs."
  },
  {
    "chunk_id": 273,
    "source_file": "GeneralBiology.pdf",
    "page": 137,
    "chunk_index_in_page": 2,
    "text": "red about 400 million years ago with cartilaginous fish. Includes about\n95% of today's fish species.\nSubclass Sarcopterygii\nfleshy-finned fishes. Fins have bones and muscles, homologous to our limbs.\nOrder Dipnoi\nlung fishes, two groups isolated when continents separated\n129"
  },
  {
    "chunk_id": 274,
    "source_file": "GeneralBiology.pdf",
    "page": 138,
    "chunk_index_in_page": 0,
    "text": "Chordates\nOrder Crossopterygii\nincludes coelacanths and rhipodistians, gave rise to amphibians, had lungs which evolved\ninto a swim bladder in bony fishes, and labyrinthodont teeth, characterized by complex\nfolding of enamel.\n• Skeleton made of bone, jaws, fins, most with scales, two-chambered heart.\n24.4.4 Class Amphibia\nmeans “both lives”, aquatic larvae, terrestrial adult Amphibians: - Legs - Lungs - Double-\nLoop Circulation - Partially Divided Heart - Cutaneous Respiration (Breathes through\nSkin)\nOrder Salientia\nfrogs (jumping) (aka Anura)\nOrder Urodela\nsalamanders (tailed)\nLabyrinthodont amphibians: oldest known amphibians, inherited characteristic teeth from\ncrossopterygii ancestor, had stocky, aquatic larvae.\nAmphibians have limbs instead of fins. Girdles and vertebral column now more substantial\nand connected, support body on legs.\nLisamphybia: no scales, “smooth”, eggs with no shell, laid in water (water-reliant)."
  },
  {
    "chunk_id": 275,
    "source_file": "GeneralBiology.pdf",
    "page": 138,
    "chunk_index_in_page": 1,
    "text": "have limbs instead of fins. Girdles and vertebral column now more substantial\nand connected, support body on legs.\nLisamphybia: no scales, “smooth”, eggs with no shell, laid in water (water-reliant).\nAmphibians gave rise to cotylosaurs, from which arose dinosaurs, turtles, lizards, and\ntherapsids.\nClass Reptilia\namniotic egg allowed freedom from water, shelled egg. (Amnion: protection). Reptiles have\nfour extra-embryonic membranes:\n• Amnion: supports aquatic environment inside egg in fluid sac.\n• Allantois: allows gas exchange and elimination of wastes.\n• Chorion: gas exchange\n• Yolk sac: only one of the four left over from amphibian ancestor\nReptiles cold-blooded, or ectothermic, meaning that their heat come from their environment.\nSometimes defined as all amniotes that are not birds or mammals.\nReptiles can be classified by skull structure into four groups:\n• Anapsid\n• Synapsid\n• Diapsid\n• Euryasid\n130"
  },
  {
    "chunk_id": 276,
    "source_file": "GeneralBiology.pdf",
    "page": 139,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\nRefers to number of holes in the skull. Cotylosaurs had Anapsid skull\nDermatocranium: from bony outer skull structure, precursor to human cranium.\nSubclass Anapsidia\nSubclass Testudinata\nturtles1, terrapins\nSubclass Diapsida\ndinosaurs2, snakes3, most stuff\nSubclass Synapsida\nOrder Therapsids\nSubclass Diapsida\nincludes Ichthyosaurs, marine reptiles convergent on dolphins; Plesiosaurs, ancient sea\nmonsters; Squamates, including lizards and snakes; and Thecodonts, which gave rise to\n• birds\n• dinosaurs\n• crocodilians\nDinosaurs: broken into two groups, based on hip structure\n• Saurischia: lizard hips (gave rise to birds [!]), ancestrally bipedal\n• Ornithischian: bird hips, ancestrally quadripedal\nCrocodilians: comefromarchosaurs, theonlyextant(stilllivingtoday)archosaurdescendant.\nAncestrally bipedal, secondarily quadripedal.\nSynapsids: refers to joined (Greek syn-, together with) parts of skull. Led eventually to\nmammals. Synapsid pelycosaur >> therapsid >> mammals"
  },
  {
    "chunk_id": 277,
    "source_file": "GeneralBiology.pdf",
    "page": 139,
    "chunk_index_in_page": 1,
    "text": "escendant.\nAncestrally bipedal, secondarily quadripedal.\nSynapsids: refers to joined (Greek syn-, together with) parts of skull. Led eventually to\nmammals. Synapsid pelycosaur >> therapsid >> mammals\nPelycosaur: Sail-backed dinosaur, legs not spread out like lizard but more pillar-like and\nunder body, allowing greater activity and competence in motion, pendulum like rather than\nconstant push-up. Teeth differentiated into different types, for pre-processing of food needed\nby higher metabolism. Skull changes, bone histology, suggestions of warm-bloodedness.\n1 http://en.wikibooks.org/wiki/turtle\n2 http://en.wikibooks.org/wiki/dinsosaur\n3 http://en.wikibooks.org/wiki/snake\n131"
  },
  {
    "chunk_id": 278,
    "source_file": "GeneralBiology.pdf",
    "page": 140,
    "chunk_index_in_page": 0,
    "text": "Chordates\nClass Aves\narose late Jurassic, early Cretaceous. Feathers, skeleton modified for flight. Feathers:\nepidermal derivative, made of keratin (like fingernails). Carpometacarpis: bears primary\nflight feathers, parallel to hand parts. Keeled sternum: breastbone, powerful one needed\nto support flight muscles. Strong, light, occasionally hollow bones. All birds lay eggs (as\ncontrasted to reptiles, which have developed live birthing over 100 independent times.) Why\nare there no live-bearing birds? Early birds had teeth, lost them. With mammals, only\nexothermic animals.\nArchaeopteryx: “ancient wing”, Jurassic bird-reptile, very dinosaur-like. Good fossils found\nin Zolenhoffen, German sandstone mine with fine sand, shows feathers clearly, found shortly\nafter Darwin’s publication and used to support his hypothesis. Thick, heavy bones and no\nsternum, bony tail, not a good flyer but did have primary flight feathers.\nArchaeornithes: includes archaeopteryx."
  },
  {
    "chunk_id": 279,
    "source_file": "GeneralBiology.pdf",
    "page": 140,
    "chunk_index_in_page": 1,
    "text": "r Darwin’s publication and used to support his hypothesis. Thick, heavy bones and no\nsternum, bony tail, not a good flyer but did have primary flight feathers.\nArchaeornithes: includes archaeopteryx.\nPaleognathae: gave rise to Australian flightless birds.\nNeognathae: remaining live birds.\nClass Mammalia\nTwo unique characteristics, or synapomorphies:\n• Hair\n• Mammary glands\n(don’t fossilize well)\nThree skeletal characteristics (fossilize)\n• Lower jaw only one bone, the dentary (several in reptiles)\n• Three bones in middle ear: malleus, incus, stapes (reptiles have one or two, never three)\n• Joint between upper and lower jaws between dentary and squamosal of skull (in reptiles\nthis joint is between other bones)\nMammals basically have a synapsid skull design inherited from ancestor\nNon diagnostic characteristics (not unique to mammals):\n• Warm-blooded\n• Skin glands: sweat glands and oil-producing sebaceous glands"
  },
  {
    "chunk_id": 280,
    "source_file": "GeneralBiology.pdf",
    "page": 140,
    "chunk_index_in_page": 2,
    "text": "ls basically have a synapsid skull design inherited from ancestor\nNon diagnostic characteristics (not unique to mammals):\n• Warm-blooded\n• Skin glands: sweat glands and oil-producing sebaceous glands\n• Large nasal cavities (because of high metabolism) Clean, warm and humidify air\n• Heterodonty (differentiated teeth)\n• Diphiodonty: two sets of teeth: baby and adult (“deciduous” teeth, drop out) (reptile\nteeth are continually replaced)\nSubclass Protheria\nmonotremes (Greek mon-, one; and trema, hole), or egg-laying mammals, have one opening\nfor excretion and urination.\n132"
  },
  {
    "chunk_id": 281,
    "source_file": "GeneralBiology.pdf",
    "page": 141,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\nSubclass Theria\nMetatheria: Marsupials (opossum, kangaroo...) Eutheria: Placentalmammals(allcommon\nmammals)\nMarsupium: (from Greek marsypion, purse or pouch). Gestation period much shorter than\nin Eutherian mammals, but after leaving the uterus the tiny offspring crawls into a pouch\nwhere it completes development latched onto a teat.\nRecent molecular (read: genetic) evidence suggests that two different mammal groups\nmay have developed live-bearing ability separately. Instead of being a “rough draft” for\nplacental-style live bearing, perhaps the marsupial pouch approach is another solution to\nthe same problem. Advantage: in tough times the parent can pitch out the offspring and\nincrease its own chance of survival.\n133"
  },
  {
    "chunk_id": 282,
    "source_file": "GeneralBiology.pdf",
    "page": 143,
    "chunk_index_in_page": 0,
    "text": "25 Tissues and Systems\n135"
  },
  {
    "chunk_id": 283,
    "source_file": "GeneralBiology.pdf",
    "page": 145,
    "chunk_index_in_page": 0,
    "text": "26 Epithelial tissue\nComes from various sources, ectodermal or endodermal material. Cell sheet lines a\nsurface or body cavity. One side, called freesurface or Apical, is exposed to\n• animal interior (forming the lumen) or\n• exterior of its body cavity.\nThe other side rests on the basal layer.\nEpithelial tissue is not penetrated by blood vessels.\nTwo categories:\n• sheets\n• glands\nClassified on two features:\n• simple, (a single layer of cells),\n• stratified, (more than one cell layer.)\nCell shape at free surface:\n• squamous (broad and flat)\n• cuboidal (spherish)\n• columnar (tall and thin)\nSimple squamous epithelium\nusually lines body cavities and vessels,alveoli, glomeruli of kidney; in blood and lymph\nvessels called endothelium; in body cavities called mesothelium (serosae): parietal serous\nmembranes line body wall, visceral serous membranes cover organ\nSimple cuboidal epithelium\nin ducts like kidney and salivary glands.\nSimple columnar epithelium"
  },
  {
    "chunk_id": 284,
    "source_file": "GeneralBiology.pdf",
    "page": 145,
    "chunk_index_in_page": 1,
    "text": "mesothelium (serosae): parietal serous\nmembranes line body wall, visceral serous membranes cover organ\nSimple cuboidal epithelium\nin ducts like kidney and salivary glands.\nSimple columnar epithelium\nnonciliated type lines digestive tract, ciliated type lines some regions of uterine tubes and\nlungs\nStratified squamous epithelium\n(important) lines mouth, esophagus,and vagina. Cells sometimes dead, flat and keratinized,\nmaking them resistant to abrasion. Stratified squamous epithelium changes to columnar\nsquamous epithelium progressively down esophagus to the stomach.\nEpidermis\n137"
  },
  {
    "chunk_id": 285,
    "source_file": "GeneralBiology.pdf",
    "page": 146,
    "chunk_index_in_page": 0,
    "text": "Epithelial tissue\nfrom epithelium. Below this is dermis, thicker and with blood vessels.\nTwo specialized epithelia:\n• pseudostratified\n• transitional\nPseudostratified epithelia\nlines the trachea (where it is ciliated)and the male urethra (where it is non ciliated), looks\nstratified but not.\nTransitional epithelia\nfound only in bladder and urinary system. As it stretches it appears to go from 6 to 3 cell\nlayers deep.\nGlandular epithelia\n(gland: group of cells that excretes something.. mostly derived from epithelium. Glands\nare classified into endocrine and exocrine by where they excrete.\nEndocrine glands\nsecrete hormones into the blood without use of ducts.\nExocrine glands\nsecrete onto the body surface or into a cavity, thru a duct. Exocrine substances include\nsweat, mucous, oil, and saliva. An exocrine gland is the liver, which secretes bile.\n138"
  },
  {
    "chunk_id": 286,
    "source_file": "GeneralBiology.pdf",
    "page": 147,
    "chunk_index_in_page": 0,
    "text": "27 Connective tissue\nThis is a “grab bag” category of diverse tissue types. Functions include binding and\nsupporting. Types include bone, cartilage, fibrous connective tissue, blood and\nadipose (fat) tissue.\nIf you took away everything in the body except the connective tissue, you’d still be able to\nsee the basic form of the body.\nForm: distinctivecellssurroundedbyacellmatrixmadeofextra-cellularfibergrounded\nin a ground substance (excluding blood)\nTypes:\n1. connectile connective tissues (can be 1. loose or 2. dense)\n2. special connective tissue (includes blood, bones and cartilage).\nFibroblasts form connective tissue proper;\nchondoroblasts form cartilage;\nosteoblasts form bone;\nand blood is formed from various sources.\nGround substance: “unstructured” material that fills space between cells and contains\nfibers. Made of\n1. interstitial fluid (bathes cells)\n2. proteoglycans (protein core with attached polysaccharides, glycoaminoglycans or GAGs"
  },
  {
    "chunk_id": 287,
    "source_file": "GeneralBiology.pdf",
    "page": 147,
    "chunk_index_in_page": 1,
    "text": "ured” material that fills space between cells and contains\nfibers. Made of\n1. interstitial fluid (bathes cells)\n2. proteoglycans (protein core with attached polysaccharides, glycoaminoglycans or GAGs\nsuch as chondroitin sulfate, keratin sulfate, and hyalronic acid, whose consistency is syrupy\nto gelatin-like)\n3. cell-adhesion proteins (connect connective tissue cells to the fibers).\nFibers of connective tissue:\n139"
  },
  {
    "chunk_id": 288,
    "source_file": "GeneralBiology.pdf",
    "page": 148,
    "chunk_index_in_page": 0,
    "text": "Connective tissue\n1. Collagen (flexible protein resistant to stretching, tensile strength, most abundant\nprotein in animals, white)\n2. elastin (rubbery, resilient protein, in dermis, lungs, blood vessels, yellow when fresh)\n3. andreticulin (like collagen).\nLoose connective tissue: found beneath skin, anchors muscles,nerves etc. Include fi-\nbroblasts, macrophages, mast cells,and adipose cells. Fibers include collagen and\nelastic fibers. Ground substance is “syrupy”. Adipose included.\nDense connective tissue: largely densely packed fibers of collagen or elastin regularly\nor irregularly arranged. Forms tendons and ligaments, coverings of muscles, capsules\naround organs and joints, and dermis of skin.\nCartilage vs. bone\nFeature Bone Cartilage\ncell type osteocytes chondrocytes\nground substance calcium phosphate chondroitin sulfate\nvascularization vascular avascular\nmicro architecture highly ordered less organized\nunits called osteons\nfibrous sheath peristeum perichondrium"
  },
  {
    "chunk_id": 289,
    "source_file": "GeneralBiology.pdf",
    "page": 148,
    "chunk_index_in_page": 1,
    "text": "ground substance calcium phosphate chondroitin sulfate\nvascularization vascular avascular\nmicro architecture highly ordered less organized\nunits called osteons\nfibrous sheath peristeum perichondrium\nCartilage: There are three cartilage types:\n1. hyaline cartilage\n2. fibrocartilage (fibrous cartilage)\n3. elastic cartilage\nHyaline cartilage: most widespread cartilage type, in adults forms articular surfaces of\nlong bones, rib tips, rings of trachea, and parts of skull. Mostly collagen, name refers to\nglassy appearance. In embryo, bones form first as hyaline cartilage, later ossifies. Found\nin tracheal rings. Few collagen fibers.\nFibrous cartilage: have lots of collagen fibers. Found in intervertebral discs, pubic\nsymphesis. Grades into dense tendon and ligament tissue.\nElastic cartilage: springy and elastic. Found in internal support of external ear and in\nepiglottis, yellow when fresh.\nChondrocites (cartilage cells) rely on diffusion for nutrients, as cartilage has no direct"
  },
  {
    "chunk_id": 290,
    "source_file": "GeneralBiology.pdf",
    "page": 148,
    "chunk_index_in_page": 2,
    "text": "tilage: springy and elastic. Found in internal support of external ear and in\nepiglottis, yellow when fresh.\nChondrocites (cartilage cells) rely on diffusion for nutrients, as cartilage has no direct\nblood supply, and no enervation (nerves). Can be loaded with calcium salts.\n140"
  },
  {
    "chunk_id": 291,
    "source_file": "GeneralBiology.pdf",
    "page": 149,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\nBone: Specialized connective tissue, calcium phosphate arranged in highly ordered unit\ncalled osteon, or Hyvercian system. Concentric rings around central canal with blood\nvessels and enervation (nerves). Bone varied, not all vertebrate bone is even cellular. Our\nconcern: simple pattern for mammals.\nLacuna (spaces in which osteocytes found); canaliculi (little canals) bigger diagonal cells,\nlayers of bone called lamellae.\nThree types of bone cells, ending in\n-blast, (mend bone)\n-cyte (fortify bone)\n-clast (tear down bone)\nClassified by\n1. appearance (spongy vs. hard)\n2. where found (outside or inside)\n3. how it is formed (endochondral cartilage model forms first and then is ossified, and\nentramembranous, bone forms directly without cartilage precursor)\nExample of endochondral bone formation: long bone begins to ossify from center shaft,\ncalcified region expands and cuts off diffusion of nutrients as bone replaces cartilage. In"
  },
  {
    "chunk_id": 292,
    "source_file": "GeneralBiology.pdf",
    "page": 149,
    "chunk_index_in_page": 1,
    "text": "cartilage precursor)\nExample of endochondral bone formation: long bone begins to ossify from center shaft,\ncalcified region expands and cuts off diffusion of nutrients as bone replaces cartilage. In\nyoung mammals, secondary ossification centers then form at bone ends, growth has stopped\nby sexual maturity as all primary bone is ossified. In other animals, bones continue growing\nthroughout their lifetime.\nThree types of intramembrous bone:\n1. dermal bone\n2. sessamoid bone\n3. perichondral bone.\nDermal boneformsskull, shoulder/pectoralgirdle, andintegument, descendedfromdermal\narmor of ancestor. Comes from mesoderm, in dermis of skin.\nSessamoid bones: form directly in tendons. Example: kneecap, also in wrist. Deals with\nstress.\nPerichondral bone means “around cartilage,” forms around cartilage or bone. Func-\ntions in bone repair and in ossification of endochondral bone.\n141"
  },
  {
    "chunk_id": 293,
    "source_file": "GeneralBiology.pdf",
    "page": 150,
    "chunk_index_in_page": 0,
    "text": "Connective tissue\nBone remodeling and repair: bone has mineral structure, and develops tiny fractures,\nwhich, under stress, can lead to larger fractures. To combat this, bone is constantly replaced.\nOsteoclasts channel through existing bone, tear down and leave behind osteoblasts\nand lacuna, leaving osteocytes. Continually resets mineral structure of bone, and is\npreventative maintenance.\nWhen bone broken, callus forms in open ends, periosteum gives rise to new bone with\ncalcium and new bone matrix, leaves irregular mend. Later, osteoblasts continue fixing over\ntime and slowly removing imperfection.\n142"
  },
  {
    "chunk_id": 294,
    "source_file": "GeneralBiology.pdf",
    "page": 151,
    "chunk_index_in_page": 0,
    "text": "28 Muscle tissue\nMesodermalinorigin,musclehasseveralfunctions: supply force for movement,restrain\nmovement, proper posture, act on viscera (internal organs) for peristalsis (moving food\ndown digestive tract), give body shape, form sphincters, (such as in esophagus, between\nstomach and intestine, large and small intestine, in anus), in sheets of muscles, affect air\nflow in and out of lungs, line blood vessels and play vital role in circulation.\nSecondary roles: heat production (shivering a specialized heat production to supplement\nmetabolism).\nMuscles co-opted to other non-original functions: sharks detect electrical field created by fish\nmuscles. Some fish formed electric organs, create current strong enough to repel predators\nor stun prey. Other fish can use field as “radar” to see things and communicate with other\nanimals. (Evolved independently in different groups).\nDifferent classifications: by color, (red or white) location, nature of nervous system"
  },
  {
    "chunk_id": 295,
    "source_file": "GeneralBiology.pdf",
    "page": 151,
    "chunk_index_in_page": 1,
    "text": "field as “radar” to see things and communicate with other\nanimals. (Evolved independently in different groups).\nDifferent classifications: by color, (red or white) location, nature of nervous system\ncontrol (voluntary or involuntary), embryonic origin, or by general microscopic ap-\npearance (striated, smooth, and cardiac.)\nStriated muscle (or skeletal muscle): under voluntary control. Individual cells called\nfibers, grouped into fascicle. Myofibrils founding one cell made of even smaller myofil-\naments. Each striated cell very long and multi-nucleated. Fibers joined end to end to\nform longer composite fibers. Sarcomeres: repeating units make up myofibrils. Two\nkinds of myofilaments, thick kind made up of myosin and thin of actin. Striations visible\nin light microscope, smaller part only with electron microscope.\nCardiac muscle: occurs only in heart. Light banding visible under light microscope.\nEach band short, principally mononucleate (occasionally dinucleate) often branched, joined"
  },
  {
    "chunk_id": 296,
    "source_file": "GeneralBiology.pdf",
    "page": 151,
    "chunk_index_in_page": 2,
    "text": "ith electron microscope.\nCardiac muscle: occurs only in heart. Light banding visible under light microscope.\nEach band short, principally mononucleate (occasionally dinucleate) often branched, joined\ntogether with intercollated discs. Involuntary. Waves of contraction spread through intercol-\nlated discs. Initiated by nerve stimulation or can originate in the heart itself (useful in heart\ntransplants.)\nSmooth muscle: no striations visible with light microscope. Almost entirely visceral\nfunction: digestion, sphincters, urogenital tracts, piloerectory muscles (make hairs stand up),\nlungs. Non-voluntary control. Slow and sustained action. Each cell mononucleate, short,\nfusiform (spindly) in shape, cells usually uniform in size.\nStriated muscle contraction: Muscle broken into units called fascicles, in units of myofibrils.\nRepeating units called sarcomeres, consisting of two kinds of myofilaments:\n1. thick, myosin filament\n2. thin, actin filament.\n143"
  },
  {
    "chunk_id": 297,
    "source_file": "GeneralBiology.pdf",
    "page": 152,
    "chunk_index_in_page": 0,
    "text": "Muscle tissue\nSarcomere: Thick and thin filaments interspersed in ordered grid.\nSliding filament theory: thick and thin filaments move past each other in opposite\ndirection, shortening length. Longer muscles contract more rapidly than short ones (see cell\nbio for details).\nMyosin molecule: two polypeptides twisted together with two globular heads at end.\nMyosin filament: many slender myosin molecules together.\nActin filament: chain of actin single, tropomyosin strands with repeated globular\ntroponin, and with actin. All play role in muscle contraction. Myocin heads have sites\nthat bind to actin. Actin filaments have many regular sites that can bind to myosin.\nTroponin has four sites:\n1. one to bind myosin\n2. one for actin\n3. one for tropomyocin\n4. one for calcium ions\nNerve signal reaches muscle, triggers release of chemical signal called neurotransmitter,\nthat diffuses across cell membrane (sarcolimic reticulum) and binds to receptors in it.\nReceptor is acetylcholine, ACH."
  },
  {
    "chunk_id": 298,
    "source_file": "GeneralBiology.pdf",
    "page": 152,
    "chunk_index_in_page": 1,
    "text": "nal reaches muscle, triggers release of chemical signal called neurotransmitter,\nthat diffuses across cell membrane (sarcolimic reticulum) and binds to receptors in it.\nReceptor is acetylcholine, ACH. When there is enough nerve signal, the message travels\nthrough t-line to sarcoplasmic reticulum to release calcium ions.\nLacking calcium, tropomyosin site blocked. In calcium, myosin binding sites exposed and\nheads bind to actin molecules, delivering force to move fibers in relation to each other.\nMyocin head then interacts with ATP to get “recocked”, if myosin still exposed then it\nfires again and results in further muscle contration. If there is no further nerve signal,\nsarcoplasmic reticulum sequesters Ca+ ions again and no recocking occurs.\nQuirari (or curare): known from movies, used in South America, blocks acetylcholine\nreceptors in cell and causes skeletal paralysis. Victim dies of asphyxiation because he can’t\nbreathe."
  },
  {
    "chunk_id": 299,
    "source_file": "GeneralBiology.pdf",
    "page": 152,
    "chunk_index_in_page": 2,
    "text": "king occurs.\nQuirari (or curare): known from movies, used in South America, blocks acetylcholine\nreceptors in cell and causes skeletal paralysis. Victim dies of asphyxiation because he can’t\nbreathe.\nDuchenne's muscular dystrophy: degeneration of sarcolema, plasma membrane of\nmuscle cell unable to release signal and quickly atrophies.\nFast and slow twitch fibers: vertebrate muscle fiber. Terms relative within one group\nof animals. Differences related to differences in enervation, type of myocin, and actin\nactivation.\nTwo parts of force generated by muscle: 1. active component 2. elastic component (energy\nstored in muscle when stretched by gravity or another force. Stored in muscle elastic tissue\naround tendons. Especially important in limb oscillation, like running, or trunk twisting,\nlike fish swimming. Up to 90% of stored elastic energy can be recovered.)\n144"
  },
  {
    "chunk_id": 300,
    "source_file": "GeneralBiology.pdf",
    "page": 153,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\nHow does a muscle match its power to its job? Two ways:\n1. rate modulation, derived from frequency of nervous stimulation of muscle, force\nincreases as frequency of stimulation increases up to point of tetanus.\n2. selective involvement of motor units, a given neuron enervates a fixed number of\nmuscle cells, (a motor unit), and force is increased by recruiting more motor units. Motor\nunits may be small, such as in eye, or larger, like in leg muscle.\nHow do muscles grow stronger?\n1. add more myofilaments, increases cross sectional area by up to 50%, more little ratchets\nworking\n2. proliferation in blood vessels and connective tissue around muscle\nMuscle strength is relative to cross sectional area, not length. Not always feasible to add\nmore cross sectional area.\nPinnate fibers: oriented obliquely (Y-shaped) to minimize muscle mass, in certain circum-\nstances, like calf muscle. Spreads muscle out.\nVelocity of shortening greater in long muscle than short. Why?"
  },
  {
    "chunk_id": 301,
    "source_file": "GeneralBiology.pdf",
    "page": 153,
    "chunk_index_in_page": 1,
    "text": "Pinnate fibers: oriented obliquely (Y-shaped) to minimize muscle mass, in certain circum-\nstances, like calf muscle. Spreads muscle out.\nVelocity of shortening greater in long muscle than short. Why? Contraction tied to relation\nbetween fibers, and to total length of muscle. Both long and short muscles reach same\npercentage of contraction in same unit time, but distance covered by the longer muscle is\ngreater.\nSynergist muscles: muscles work together to produce motion in same general direction.\nBicep shares work with brachialis.\nAntagonist muscles: muscles that oppose each other. Bicep pulls forearm in, triceps pulls\nit back out.\nOrigin vs. insertion: origin is the end of the muscle that more fixed in its attachment to\nthe body. The more movable end called insertion.\nFixators: muscles that act to stabilize a joint or lever system. Like upper arm when you\nclench your fist hard.\nFlexors and extensors: appliedmainlytolimbs. Flexorbendsonepartrelativetoanother"
  },
  {
    "chunk_id": 302,
    "source_file": "GeneralBiology.pdf",
    "page": 153,
    "chunk_index_in_page": 2,
    "text": "rtion.\nFixators: muscles that act to stabilize a joint or lever system. Like upper arm when you\nclench your fist hard.\nFlexors and extensors: appliedmainlytolimbs. Flexorbendsonepartrelativetoanother\nabout limb, extensor straightens it.\nAdductor and abductor: adductor draws a limb toward the ventral surface. Abductor\nmoves limb away from ventral surface. (Adduct: drawn toward; abduct: carry away).\n145"
  },
  {
    "chunk_id": 303,
    "source_file": "GeneralBiology.pdf",
    "page": 155,
    "chunk_index_in_page": 0,
    "text": "29 Vertebrate digestive system\nFunctions to break down food into molecules small enough to absorb, or pass across digestive\nmembrane.\nDigestive tract: tube extending from lips of mouth to anus or cloacae in bird, reptile or\nmonotreme.\nLumanal glands: empty into inner body cavity (lumen: inner surface).\nTract divided into three main regions: 1. buccal cavity 2. pharynx 3. alimentary canal\nAlimentary canal divided into four regions: 1. esophagus 2. stomach 3. small intestine 4.\nlarge intestine\nAccessory digestive glands, outside digestive tract proper, secrete into lumen of tract\nthrough ducts. Includes the salivary glands, liver and pancreas.\nBuccal cavity,whichincludespalateandtongue,developsfrominfoldingofstomadeum,\nor second opening of blastula, whereas the rest of the digestive tract develops from the\nprimitive gut.\nTeeth: capture and hold prey. In mammals in particular further process and break down\nfood into small particles, increasing surface area available for enzymatic action."
  },
  {
    "chunk_id": 304,
    "source_file": "GeneralBiology.pdf",
    "page": 155,
    "chunk_index_in_page": 1,
    "text": "velops from the\nprimitive gut.\nTeeth: capture and hold prey. In mammals in particular further process and break down\nfood into small particles, increasing surface area available for enzymatic action.\nTooth anatomy: 1. crown projects above gum, 2. root below gum, 3. enamel is outer\ncoating of crown, hardest surface in body, of epideral origin 4. dentin, below enamel,\nbone-like and forms bulk of tooth, is harder than bone and contains nerves and blood vessels.\n(Remember that mammals are heterodontic, with different types of teeth).\nPharynx: air passage for adult, gill slits in embryo. Important in lower vertebrates, site of\ngills. Features derived from pharyngeal region: first pharyngeal pouch gives rise to parts\nof the ear, other pouches give rise to various other structures.\nAlimentary canal: epithelium lines lumen, glands secrete into lumen, longitudinal and\ncircular muscles help digestive movements (peristalsis).\nEsophagus: tube carries food from mouth to stomach."
  },
  {
    "chunk_id": 305,
    "source_file": "GeneralBiology.pdf",
    "page": 155,
    "chunk_index_in_page": 2,
    "text": "ures.\nAlimentary canal: epithelium lines lumen, glands secrete into lumen, longitudinal and\ncircular muscles help digestive movements (peristalsis).\nEsophagus: tube carries food from mouth to stomach. Expands to fit large bolus (lump\nof chewed food). Secretes mucus for lubrication. Birds have crop for storage, enlargement\nof esophagus.\nEpiglottis: keeps food out of air tube, an evolutionary “kludge,” or fix.\nStomach. Absorbs water, alcohol, nutrients, uses gastric juice with enzymes, mucous, HCl,\nreleased by chief and parietal cells (release protein enzymes) in gastric pits. Rugae: folds\nof stomach, disappear when full. Sphincter at both ends of stomach, control food passage.\nChyme: semi-digested food released to small intestine.\n147"
  },
  {
    "chunk_id": 306,
    "source_file": "GeneralBiology.pdf",
    "page": 156,
    "chunk_index_in_page": 0,
    "text": "Vertebrate digestive system\nSmall intestine: three regions, duodenum, jejunum, and ileum.\nDuodenum site of most intestinal digestion. Jejunum and ileum do most of intestinal\nabsorption. Ileum ends with another sphincter, ileocolic valve or ileosecal valve. Structure:\nCircular folds covered with villi (singular is villus).\nVilli: finger-likecellularprojections,coveredwithmicrovilli,tinyprojectionswhichincrease\nsurfacearea. Increasessurfaceareaby900x,speedsdigestion(breakdown)andabsorption\n(taking in nutrients).\nLarge intestine: largerdiameter, shorterlengththansmallintestine. Novilli. Inmammals,\nforms large gentle loop, colon, empties into straight region, rectum, empties into outside\nworld through anal sphincter. Colon: absorbs water left over, also absorbs vitamins released\nby bacteria which live there (vitamin K).\nFood: made up of 1. proteins, 2. fats, 3. carbohydrates 4. fibrous material.\nDigestive system breaks foods down. Proteins must be broken to amino acids to be\nabsorbed."
  },
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    "page": 156,
    "chunk_index_in_page": 1,
    "text": "ia which live there (vitamin K).\nFood: made up of 1. proteins, 2. fats, 3. carbohydrates 4. fibrous material.\nDigestive system breaks foods down. Proteins must be broken to amino acids to be\nabsorbed. Polysaccharides to monosaccharides, lipids to fatty acids and monoglyc-\nerides to absorb.\nSalivary glands in mouth, saliva contains mucous, salt and a few enzymes (amalase, begins\nstarch breakdown). Snake venom from oral gland, mixture of toxins and digestive enzymes.\nBreaks down blood vessels and disables nervous system.\nStomach enzymes: releasedininactiveform, zymogene, convertstoactiveforminlumen\nof gut. Transformation is triggered by another enzyme, or the stomach’s low pH. Pepsin\nsecreted as pepsinogen (-ogen means primitive form). Stomach glands secrete up to two or\nthree liters a day of gastric juice, which is reabsorbed.\nChyme released to duodenum.\nSmall intestine has two major accessory glands: 1. pancreas 2. liver"
  },
  {
    "chunk_id": 308,
    "source_file": "GeneralBiology.pdf",
    "page": 156,
    "chunk_index_in_page": 2,
    "text": "e form). Stomach glands secrete up to two or\nthree liters a day of gastric juice, which is reabsorbed.\nChyme released to duodenum.\nSmall intestine has two major accessory glands: 1. pancreas 2. liver\nPancreas has endocrine and exocrine functions, releases large amounts of carbonate to\nneutralize acidic chyme, as intestinal enzymes work in neutral pH, and stuff to break down\nlipids and starch (zymogens, like tripsin)\nLiver releases bile. Bile made from cholesterol, stored in gall bladder, released in\nduodenum, emulsifies fats.\nEmulsify: keeps fats in tiny drops, which are suspended, increasing surface area and action\nof lipases. Protein and carbohydrates absorbed in intestine, taken to liver for processing.\nFatty acids go to lymphatic system\nAppendix: vestigial remnant. Much variation in digestive systems within mammals:\nherbivore, carnivore, insectivore, non-ruminant herbivore.\nRumen: four-chambered stomach of animals like cows (ruminant herbivores). Cellulose"
  },
  {
    "chunk_id": 309,
    "source_file": "GeneralBiology.pdf",
    "page": 156,
    "chunk_index_in_page": 3,
    "text": "ant. Much variation in digestive systems within mammals:\nherbivore, carnivore, insectivore, non-ruminant herbivore.\nRumen: four-chambered stomach of animals like cows (ruminant herbivores). Cellulose\nresistant to digestion, rely on microorganisms to break down cellulose. Some bacteria,\nprotists and fungi can break down cellulose, almost no animals can. Bacteria break down\ncellulose in rumen, to be taken back to the mouth to chew their cud (ruminate). Later cow\nswallows to proceed with digestion. (Horses not like this).\n148"
  },
  {
    "chunk_id": 310,
    "source_file": "GeneralBiology.pdf",
    "page": 157,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\nCoprophagy: rabbits and other animals eat their own feces for the nutritious products of\nthe cecum.\n149"
  },
  {
    "chunk_id": 311,
    "source_file": "GeneralBiology.pdf",
    "page": 159,
    "chunk_index_in_page": 0,
    "text": "30 Circulatory system\nCirculatory system functions\n1. Transportation\na. Respiration: gas exchange (O2 and CO2), overcomes limited rate\nof\ndiffusion\nb. Nutrition:<br>\nc. Excretory: (remove metabolic wastes)<br>\n2. Regulation\na. Transport hormones<br>\nb. Regulate body temperature<br>\nc. Protection<br>\ni. Blood clotting<br>\nii. Immune system (carries white blood cells)\nVasodilation: allows heat loss across epidermis, as seen in elephant ears, takes more blood\nto surface of body, sweating may accompany\nCountercurrent heat exchange: used by dolphins in fins to conserve heat in cold water.\nVeins surround an artery, and blood returning to body absorbs heat from blood traveling\nout from body to fin, minimizing heat loss. Used by dogs in feet, etc.\nBlood made of 1. plasma and 2. formed cellular elements (red and white blood cells,\nand platelets).\nPlasma makes up 55% of blood volume. Cellular elements make up the other 45%."
  },
  {
    "chunk_id": 312,
    "source_file": "GeneralBiology.pdf",
    "page": 159,
    "chunk_index_in_page": 1,
    "text": "by dogs in feet, etc.\nBlood made of 1. plasma and 2. formed cellular elements (red and white blood cells,\nand platelets).\nPlasma makes up 55% of blood volume. Cellular elements make up the other 45%.\nPlasma makeup: 90% water, 7-8% soluble proteins (albumin maintains blood osmotic\nintegrity, others clot, etc.) 1% electrolytes 1% elements in transit\nRed blood cell (erythrocyte): contains hemoglobin, functions in oxygen transport. In\nmammals, red blood cells lose nuclei on maturation, and take on biconcave, dimpled, shape.\nNo self repair, live 120 days. About 1000x more red blood cells than white blood cells.\nAbout 7-8 micrometers in diameter.\n151"
  },
  {
    "chunk_id": 313,
    "source_file": "GeneralBiology.pdf",
    "page": 160,
    "chunk_index_in_page": 0,
    "text": "Circulatory system\nHematocrit: proportion of blood volume that is occupied by cells, about 43% in humans\non average. 48% for men and 38% for women.\nWhite blood cells (leukocytes): Nucleated, about 10-14 micrometers in diameter, com-\nmonly amoeboid, escape circulatory system in capillary beds. Include basophils, eosinophils,\nneutrophils, monocytes, B- and T-cell lymphocytes.\nPlatelets (thrombocytes) Membrane bound cell fragments in mammals, no nucleus. In\nnon-mammals, platelet role replaced by nucleated cells. Accumulate at site of broken blood\nvessels, form clots. Bud off special cells in bone marrow. 1-2 micrometers in diameter. 7-8\nday life span, 1/10 or 1/20 as abundant as white blood cells.\nArteries: carry blood away from heart. Smallest tubes called arterioles, feed blood to\ncapillaries.\nVeins: return blood to heart. Smallest veins called venules.\nStructureofarteriesandveins, listedfrominside(lumen)out: 1. epithelium(endothelium),\n2. elastic connective tissue fibers, 3."
  },
  {
    "chunk_id": 314,
    "source_file": "GeneralBiology.pdf",
    "page": 160,
    "chunk_index_in_page": 1,
    "text": "o\ncapillaries.\nVeins: return blood to heart. Smallest veins called venules.\nStructureofarteriesandveins, listedfrominside(lumen)out: 1. epithelium(endothelium),\n2. elastic connective tissue fibers, 3. smooth muscle, 4. connective tissue. Arteries\nhave thicker elastic layer than do veins.\nCapillaries, where exchange of materials occurs, are very thin and narrow, and red blood\ncells pass through single file. Capillaries are tiny but numerous, and their total volume is\ngreater than that of supplying arteries.\nBlood velocity drops in capillaries, picks back up in veins. Pressure highest in arteries, lower\nin capillaries and arteries.\nOsmotic pressure draws interstitial fluid from blood in arterioles, but replaces it in venules.\nOne-way valvesmeanthatbloodcanflowonlyoneway, workswithresidualbloodpressure\nand compression by skeletal muscles. Low pressure in thoracic cavity caused by breathing\nalso helps move blood.\nLymphatic system: part of the immune system, a one-way, or open, system."
  },
  {
    "chunk_id": 315,
    "source_file": "GeneralBiology.pdf",
    "page": 160,
    "chunk_index_in_page": 2,
    "text": "albloodpressure\nand compression by skeletal muscles. Low pressure in thoracic cavity caused by breathing\nalso helps move blood.\nLymphatic system: part of the immune system, a one-way, or open, system. Takes up\ninterstitial fluid not taken up by venules.\nLymphatic structures:\n1. lymphatic capillaries\n2. lymphatic vesicles\n3. lymph nodes\n4. lymphatic organs (spleen and thymus)\nLymph: movement in mammals through one-way valves, similar to blood movement in\nveins. (Some non-mammals have lymphatic hearts of unknown embryonic origin. Frogs and\nsalamanders have several.) Lymph rejoins cardiovascular system into a large vein near the\nheart via single large thoracic duct.\n152"
  },
  {
    "chunk_id": 316,
    "source_file": "GeneralBiology.pdf",
    "page": 161,
    "chunk_index_in_page": 0,
    "text": "Subphylum Vertebrata\nAs lymph passes through system, passes lymphocytes, second part of immune system.\nHeart: pumps blood, design varies between animals. In adult mammal,four chambers form\ntwo separate circulations\n1. pulmonary circulation to and from lungs and\n2. systemic circulation to and from tissues of body.\nEverything in the heart comes in pairs: 2 atria, 2 ventricles (left and right).\nDiagrams usually drawn as though animal were on its back.\nPattern of blood flow through heart: blood returning from major veins (vena cava)\nentersrightatrium, contractiontheredeliversbloodtorightventriclethroughatricuspid\nvalve, one of atrial ventricular valves (AV valve). Contraction of right ventricle drives blood\nthrough semi lunar valve into pulmonary circuit and to lungs.Blood return to heart in\npulmonary veins, is oxygenated. Goes to left atrium, which contracts and delivers blood\nto left ventricleby way of aortic semi-lunar valve, then goes to systemic circulation."
  },
  {
    "chunk_id": 317,
    "source_file": "GeneralBiology.pdf",
    "page": 161,
    "chunk_index_in_page": 1,
    "text": "Blood return to heart in\npulmonary veins, is oxygenated. Goes to left atrium, which contracts and delivers blood\nto left ventricleby way of aortic semi-lunar valve, then goes to systemic circulation.\nBoth atria and ventricles contract in unison, left is more powerful than right (to all system\nvs. just lungs).\nSystole: heart contraction, diastole: heart relaxed\nTiming of heart contraction: ventricles rebound to relaxed shape (diastole), and semi-\nlunar valves close. Both atria(singular: atrium) fill with blood coming from pulmonary\nand systemic circulations.Pressure rises in the atria and blood begins to move into the\nventricles.The atria then contract, forcing more blood into the ventricles. There is a pause,\nthen ventricles contract. This raises ventricle pressure, atrio-ventricular(AV) valves\nshut and semi-lunar valves open, forcing blood from the left ventricle into the major arteries\nand from the right ventricle into the aorta."
  },
  {
    "chunk_id": 318,
    "source_file": "GeneralBiology.pdf",
    "page": 161,
    "chunk_index_in_page": 2,
    "text": "his raises ventricle pressure, atrio-ventricular(AV) valves\nshut and semi-lunar valves open, forcing blood from the left ventricle into the major arteries\nand from the right ventricle into the aorta.\nControl for this action doesn’t rely on nervous stimulation, has intrinsic rhythmicity, called\nmyogenic. This is the case in mammal as well as in mollusk hearts. Other animals have\nneurogenic hearts that rely on nervous stimulation for heart action, originating in the\ncardiac ganglion.\nThe rhythmicity of mammalian heart relies on the sino-atrial (SA)node, or pacemaker.\nThis is a phylogenic (based on evolutionary history) remnant of an early vertebrate heart\nthat had one more chamber than modern hearts.\nHow the heart contracts: waves of depolarization start in SA node and spread\nthrough atria. Connectile tissue pauses the spread of depolarization at the atrial ventricular\nnode. Signal continued by bundle branches to lower ventricle, begins to stimulate\nheart to contract."
  },
  {
    "chunk_id": 319,
    "source_file": "GeneralBiology.pdf",
    "page": 161,
    "chunk_index_in_page": 3,
    "text": "read\nthrough atria. Connectile tissue pauses the spread of depolarization at the atrial ventricular\nnode. Signal continued by bundle branches to lower ventricle, begins to stimulate\nheart to contract. Contraction starts at bottom of heart at heart apex,then signals spread\nthrough heart.\nMedulla (in the brain) controls autonomic nervous system. (The medulla is part of\nthe brain, is continuous with the spinal cord, and controls involuntary actions of the\nbody). Sympatheticcardiacacceleratorconnectstospinalcord,usesnorepinephrine\nto signal. Parasympathetic cardio-inhibitory center reaches heart through Vagus\n153"
  },
  {
    "chunk_id": 320,
    "source_file": "GeneralBiology.pdf",
    "page": 162,
    "chunk_index_in_page": 0,
    "text": "Circulatory system\nnerve, usesacetylcholine to signal. Hyperpolarizes membrane to inhibit heart contraction.\n(Autonomic nervous system: two parts working in contra to control from both sides.)\nDominant effect here is inhibitory. If we cut Vagus nerve, heart rate promptly rises about\n25 bpm.\n154"
  },
  {
    "chunk_id": 321,
    "source_file": "GeneralBiology.pdf",
    "page": 163,
    "chunk_index_in_page": 0,
    "text": "31 Respiratory system\nIn humans and other animals, for example, the anatomical features of the respiratory system\ninclude airways, lungs, and the respiratory muscles.\nOtheranimals,suchasinsects,haverespiratorysystemswithverysimpleanatomicalfeatures,\nand in amphibians even the skin plays a vital role in gas exchange.\nPlants also have respiratory systems but the directionality of gas exchange can be opposite\nto that in animals. The respiratory system in plants also includes anatomical features such\nas holes on the undersides of leaves known as stomata.\nIn mammals, the diaphragm divides the body cavity into the\nabdominal cavity: contains the viscera (e.g., stomach and intestines)\nthoracic cavity: contains the heart and lungs.\nRespiratory tree: terminates in alveolus, alveoli. Respiratory bronchioles branch into\nalveolar ducts and into alveoli. Alveolus: microscopic air sacs, 300 million of these in human\nlungs. Total surface area large. Gas diffuses micrometer, very tiny distance."
  },
  {
    "chunk_id": 322,
    "source_file": "GeneralBiology.pdf",
    "page": 163,
    "chunk_index_in_page": 1,
    "text": "ry bronchioles branch into\nalveolar ducts and into alveoli. Alveolus: microscopic air sacs, 300 million of these in human\nlungs. Total surface area large. Gas diffuses micrometer, very tiny distance.\nNervous System\nComposed of tissues designed to integrate sensory information and direct a coordinated\nresponse to the environment.\nBasic unit of the nervous system is the neuron1, a highly specialized cell that uses both\nelectrical and chemical processes to communicate. Neurons \"listen\" to sensory organs or\nother neurons, and can simultaneously \"hear\" from 1 to hundreds of inputs simultaneously.\nLikewise, a neuron can \"talk\" to other neurons or cells that can create an action, like muscle\ncells or glands.\nNeurons are outnumbered in the nervous system by glia. Glia were once thought to only play\na supportive role in helping neurons survive; today we know that they also are important\nparticipants in the communication process. Glial cells include astrocytes, ependymal cells,"
  },
  {
    "chunk_id": 323,
    "source_file": "GeneralBiology.pdf",
    "page": 163,
    "chunk_index_in_page": 2,
    "text": "ought to only play\na supportive role in helping neurons survive; today we know that they also are important\nparticipants in the communication process. Glial cells include astrocytes, ependymal cells,\nand a cell that has a macrophage like function. There are also oligodendocytes and Schwann\ncells that provide a myelin sheath.\n1 http://en.wikipedia.org/wiki/Neuron\n155"
  },
  {
    "chunk_id": 324,
    "source_file": "GeneralBiology.pdf",
    "page": 164,
    "chunk_index_in_page": 0,
    "text": "Respiratory system\n31.1 Neuron structure\nFigure 9 Neuron\n• Dendrite will receive information from other axons\n• Stoma is the neuron body and contains typical cell parts including the mitochondria and\nnucleus. This is where neurotransmitters are synthesized.\n• Axon hillock is where the cell body and the axon meet.\n• Axon is surrounded by myelin.\n• Contains nodes of Ranvier\nTypes of axons include unipolar, bipolar, pseudopolar.\nAction potentials results from excitatory stimuli received from the dendrites that results\nin a signal that travels down the axon. On the cellular level, there is a Na+ influx via\nchannels causing a depolarization of the cell. Once those channels close, the slower opening\nK+ channels will open resulting in hyperpolarization by the cell.\nSynapses\nNeurotransmitters allow a chemical signal to be sent from one neuron to the other. Neuro-\ntransmitters must bypass a physical gap called the synapse. Examples of neurotransmitters"
  },
  {
    "chunk_id": 325,
    "source_file": "GeneralBiology.pdf",
    "page": 164,
    "chunk_index_in_page": 1,
    "text": "the cell.\nSynapses\nNeurotransmitters allow a chemical signal to be sent from one neuron to the other. Neuro-\ntransmitters must bypass a physical gap called the synapse. Examples of neurotransmitters\ninclude acetylcholine, epinephrine, and glutamate.\nExample : Neuromuscular synapses\n156"
  },
  {
    "chunk_id": 326,
    "source_file": "GeneralBiology.pdf",
    "page": 165,
    "chunk_index_in_page": 0,
    "text": "Central nervous system\nCircuits / Nuclei / Ganglia\n31.2 Central nervous system\nCentral nervous system includes the brain and the spinal cord.\nBrain There are four lobes of the brain.\n• Frontal lobe - decision making\n• Parietal lobe\n• Temporal lobe\n• Occipital lobe - vision\nThe areas of the brain are also dedicated to different functions.\n• Precentral gyrus\n• Postcentral gyrus\nProtection The CNS is protected by three layers - the pia mater, the arachnoid mater, and\nthe dura mater. Protection also comes from the circulation of cerebral spinal fluid (CSF).\nCSF helps to float the brain and also provide nutrients to both the brain and the spinal\ncord. CSF is synthesized from the choroid plexus of the lateral ventricles. In total, there are\nfour ventricles - 2 lateral ventricles, a 3rd, and 4th ventricle.\n31.3 Peripheral nervous system\nThe peripheral nervous system is broken down into two sub-systems, the somatic nervous\nsystem and the autonomic nervous system."
  },
  {
    "chunk_id": 327,
    "source_file": "GeneralBiology.pdf",
    "page": 165,
    "chunk_index_in_page": 1,
    "text": "al ventricles, a 3rd, and 4th ventricle.\n31.3 Peripheral nervous system\nThe peripheral nervous system is broken down into two sub-systems, the somatic nervous\nsystem and the autonomic nervous system.\nANS - Autonomic Nervous System The ANS has two components - parasympathetic and\nsympathetic.\nThe sympathetic nervous system is the \"fight or flight\" or fright response and results in an\nincreased heart rate, increased rate of breathing, and an elevated blood glucose level. There\nis also decreased digestion. The second neurotransmitter is epinephrine. In this case, the\nfirst neuron is short and the second neuron is long.\nThe parasympathetic nervous system is the rest and digest system.\nDrugs must be able to pass the blood brain barrier to have an effect on the CNS. Drugs act\nby affecting the neuron and how likely it is to fire an action potential.\nStroke occurs when there is a blood clot that goes to the brain and prevent blood flow.\n157"
  },
  {
    "chunk_id": 328,
    "source_file": "GeneralBiology.pdf",
    "page": 167,
    "chunk_index_in_page": 0,
    "text": "32 Sensory systems\nCategorized by\n1. nature of stimulus, such as mechanical, chemicalor light stimulus, and\n2. where stimulus received, such as outside (exteroceptors,such as the eye and\nskin temp receptors) or insidebody (interoceptors, such as blood body tem-\nperature receptors).\nTransduction of sensory input into signal. Means to “carry across”,signal transduced, or\ncarried, from environment into nervous signal.\nThree sensory processes we cover\n1. taste and smell (chemoreception)\n2. gravity and movement\n3. light\n32.1 Taste and smell (chemoreception)\nFound in mammal nose and mouth, fly feet, fish bodies, moth antennae.\nPapilla: bumps on tongue, contain taste buds down between. Sweet, sour, salty and bitter.\nSome act directly by ion channels, others act indirectly. Other “taste” sensations really\nsmell.\nSmell: received in nasopharynx. Airborne molecules go into solution on moist epithelial\nsurface of nasal passage. Approximately 1000 genescode for sensory neuron receptors. “Fried"
  },
  {
    "chunk_id": 329,
    "source_file": "GeneralBiology.pdf",
    "page": 167,
    "chunk_index_in_page": 1,
    "text": "tions really\nsmell.\nSmell: received in nasopharynx. Airborne molecules go into solution on moist epithelial\nsurface of nasal passage. Approximately 1000 genescode for sensory neuron receptors. “Fried\nonions” odor not one receptor but a mixture of many odors registered in our mind as one.\nVery sensitive, habituates rapidly (don’t notice a smell after a bit). Odor sensation has\nrelatively unfiltered root to higher brain centers.\nSnakes more chemosensory focused than us.\n32.2 Response to gravity and movement\nRegistered in inner ear. Three semicircular canals loop in three planes at right angles\nto each other, responsible for transduction of movement messages. Method: hair cells\n159"
  },
  {
    "chunk_id": 330,
    "source_file": "GeneralBiology.pdf",
    "page": 168,
    "chunk_index_in_page": 0,
    "text": "Sensory systems\ndeformed by gelatinous membrane. Vestibular apparatus, gives us perception of gravity\nand movement. Due to physical response, not chemical binding.\nCochlea: bony, coil shaped part of inner ear, where hearing occurs.\nSound enters through auditory canal, vibrates tympanic membrane,moving three bones\nof middle ear (malleus, incus, and stapes)against oval window opening in front of cochlea.\nCochlea has three fluid filled ducts, one of these the organ of Corti. Sound waves in air\ngo to vibration in organ of Corti; fluid tickles hair cells, which register the movement\nalong basilar membrane in cochlea. Different sound frequencies move different portions\nof basilar membrane. Hearing loss due to loss of hair cells.Humans normally smell more\nthan 300 odors in a day(Facts and Truth).\nTransduction of sound accomplished throgh physical deformation,not chemical binding.\n32.3 Vision\nLight enters pupil, focused by lensonto retina.\nSclera: hardened part behind retina."
  },
  {
    "chunk_id": 331,
    "source_file": "GeneralBiology.pdf",
    "page": 168,
    "chunk_index_in_page": 1,
    "text": "Facts and Truth).\nTransduction of sound accomplished throgh physical deformation,not chemical binding.\n32.3 Vision\nLight enters pupil, focused by lensonto retina.\nSclera: hardened part behind retina.\nOptic nerves and neurons attached to retina. Blind spot where optic nerve attaches, has\nno receptors.\nTwo types of photoreceptors\n1. rods - black and white low-light vision, 100 million in each retina in humans.\n2. cones - color vision, work best under better illumination. 3 million in each retina.\nFovia: region of most acute vision, has most of the cones, few rods.\nTransduction process of light to signal a molecular change, to light absorbing molecule\ncalled photopigment. Located in outer parts of rods and cones in pigment discs. The rod\nphotopigment is called rhodopsin,cone has three photopigments, called photopsins. This\nmolecular change initiates pathways to result in action potential in downstream neuron\nleading to vision center in brain.Parul Godika"
  },
  {
    "chunk_id": 332,
    "source_file": "GeneralBiology.pdf",
    "page": 168,
    "chunk_index_in_page": 2,
    "text": "d rhodopsin,cone has three photopigments, called photopsins. This\nmolecular change initiates pathways to result in action potential in downstream neuron\nleading to vision center in brain.Parul Godika\nEach of the three photopsins has a different peak of sensitivity: blue,green or red, and\nchanges isometric form (from cisto trans) based on light from a particular wavelength\nrange. Color blindness:inherited lack of one or more types of these cones. Gene carried on X\nchromosome, therefore more common in men than women.\n32.4 Homeostasis\nIs a very important part of everyone's and everything's lives. Defined as dynamic con-\nstancy of internal environment, maintenance of a relatively stable environment inside\nan organism usually involving feedback regulation.\n160"
  },
  {
    "chunk_id": 333,
    "source_file": "GeneralBiology.pdf",
    "page": 169,
    "chunk_index_in_page": 0,
    "text": "Osmotic environments and regulations\nHomeostasis is maintained in face of\n1. a varying external environment, or\n2. a non-ideal, constant external environment (as with the penguin).\nDeals with temperature, pH, chemical concentrations,pressure, oxygen levels.\nOccurs through negative feedback loops.\nVarious forms: simple thermostat in house turns off heater when above a certain temperature\nand on when below a certain temperature Involves stimulus, sensor,integrating center,\neffector and response.\nMore efficient control has two sensors and two effectors. Can be antagonistic to each\nother, such as, one cools, the other heats.\nPrecise control through proportional control, not all-or-none, furnace comes on a little\nbit if the house a bit cold. Examples in humans: vasoconstriction, change in metabolic rate,\nshivering. Physiological responses for high body temp: blood goes to body surface, sweating,\nbehavioral changes (get out of sun)."
  },
  {
    "chunk_id": 334,
    "source_file": "GeneralBiology.pdf",
    "page": 169,
    "chunk_index_in_page": 1,
    "text": "cold. Examples in humans: vasoconstriction, change in metabolic rate,\nshivering. Physiological responses for high body temp: blood goes to body surface, sweating,\nbehavioral changes (get out of sun).\nPositive feedback loop: effector increases deviation from set point. Amplifies reaction.\nLike blood clotting process, uterine contraction during childbirth. Negative feedback must\nexist at some point for control.\n32.5 Osmotic environments and regulations\n1. Marine invertebrates\na) fully marine invertebrates (not intertidal or estuarine) osmoconformers (set\ninternal environment same as environment, no net flow of ions) in a stenohaline\n(narrow non-changing salt level) environment\nb) Coastal, intertidal, estuarine (ion levels fluctuate) invertebrates.Partly osmo-\nconfomers, partly osmoregulators in a euryhaline (wide salt level variation)\nenvironment (ex: shore crab, regulates sometimes when salt levels in environment\nget real low).\n2. Freshwater animals."
  },
  {
    "chunk_id": 335,
    "source_file": "GeneralBiology.pdf",
    "page": 169,
    "chunk_index_in_page": 2,
    "text": "smo-\nconfomers, partly osmoregulators in a euryhaline (wide salt level variation)\nenvironment (ex: shore crab, regulates sometimes when salt levels in environment\nget real low).\n2. Freshwater animals. Here, environment has lower solute concentrations than do\nliving organisms so water tends to flow in and solutes out.\na) Freshwater fish (bony) dilute urine, and gills actively take up ions (NaCl)\nb) Freshwater invertebrates: same situation as freshwater fish but with different\nstructures\nc) Freshwater amphibians: active uptake of salts across their skin\n3. Marine fishes: Here the environment has a higher solute concentration than does\nthe organism so water tends to flow out and ions in.\na) Bony fishes: actively secrete salts (NaCl) across gills, absorb water across gut\nwall, their kidney (unlike mammalian kidney) is unable to generate concentrated\nurine so glomerulus is reduced, active tubular secretion of MgSO\n4"
  },
  {
    "chunk_id": 336,
    "source_file": "GeneralBiology.pdf",
    "page": 169,
    "chunk_index_in_page": 3,
    "text": "e salts (NaCl) across gills, absorb water across gut\nwall, their kidney (unlike mammalian kidney) is unable to generate concentrated\nurine so glomerulus is reduced, active tubular secretion of MgSO\n4\nb) cartilaginous fishes (and coelacanth): blood retains urea and trimethylamineoxide\nto increase its osmolality to that of seawater\n161"
  },
  {
    "chunk_id": 337,
    "source_file": "GeneralBiology.pdf",
    "page": 170,
    "chunk_index_in_page": 0,
    "text": "Sensory systems\n4. Terrestrial animals: here problem is loss of water to a drier environment, and\nregulation of salt levels.\na) water loss adaptations\nb) concentrated exception of salts and nitrogenous wastes\nHypoosmotic: having less osmotic potential than nearby fluid\nHyperosmotic: having more osmotic potential than nearby fluid\nIsoosmotic: having equal osmotic potential than nearby fluid\nGlomerulus: reduces volume of kidney\nFish started in salt water, spread to fresh water, later reinvaded salt-water environment.\nTerrestrial animal water sources:\n1. drinking\n2. moist foods\n3. from breakdown of metabolic molecules like fats. (Desert kangaroo rats get 90% of their\nwater from metabolism.)\nSecretion of nitrogenous wastes: from metabolism of amino acids, amino group has to be\nremoved in one of three basically interchangeable chemical forms:\n1. ammonia (aquatic life)\n2. urea (mammals)\n3. uric acid (birds)\nAmmonia very toxic, soluble, and cheap to produce. Easy to expel for bony fishes."
  },
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    "page": 170,
    "chunk_index_in_page": 1,
    "text": "e of three basically interchangeable chemical forms:\n1. ammonia (aquatic life)\n2. urea (mammals)\n3. uric acid (birds)\nAmmonia very toxic, soluble, and cheap to produce. Easy to expel for bony fishes.\nUrea: low toxicity, good solubility, more costly to lose as it contains other groups on it.\nMust be released in solution, water cost.\nUric acid (white part of bird poo) low toxicity, insoluble, secreted with little water loss,\nmore costly side groups lost than the others.\nMammalian kidney: Structure: fist-sized organ in lower back. About 1/5 of blood from\naorta at any time is passing through kidneys. Blood passes through kidney many times a\nday.\nNephron: structural and functional unit of kidney.\nBowmans capsule: funnel-like opening, contains primary filter, the glomerulus.\nProximal convoluted tubule: receives stuff from Bowmans capsule.\nLoop of Henle: descends and ascends.\n162"
  },
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    "text": "Osmotic environments and regulations\nVasa recta: capillaries that surround the Loop of Henle.\nGlomerulus: main filter of the nephron, located within the Bowman's capsule\nKidney properties and processes important to its function\n1. Active transport of solutes from one fluid to another against a concentration gradient,\nNa+ actively transported out of filtrate by cells of the thick ascending loop of Henley into\nthe interstitial fluid\n2. Passive movement of solutes and water from one fluid to another(down a concen-\ntration gradient), movement of water and NaCl out of descending loop of Henley into\ninterstitial fluid.\n3. Differential permeability of cells in different regions of the nephron to movement\nof water and solutes, ascending thick look is impermeable to water, descending portion is\npermeable to water\n4. Hormonal control of that permeability, antidiuretic hormone(ADH) increases\npermeability of collecting due to water, resulting in reduced volume of filtrate and thus"
  },
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    "page": 171,
    "chunk_index_in_page": 1,
    "text": "g portion is\npermeable to water\n4. Hormonal control of that permeability, antidiuretic hormone(ADH) increases\npermeability of collecting due to water, resulting in reduced volume of filtrate and thus\nmore concentrated urine.\n5. Increasing solute concentration in the interstitial fluid of the kidney, from the\ncortex to the deepest medulla, maintained by a countercurrent multiplier mechanism\n163"
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    "text": "33 Additional material\n• Francis Crick1 chemist and molecular biologist, discovered structure of DNA molecule\n• Charles Darwin2 the father of the science of evolutionary biology\n• Richard Dawkins3 zoologist and biology populariser\n• Stephen Jay Gould4 paleontologist and science populariser\n• J.B.S. Haldane5 geneticist and evolutionary biologist, founded population genetics and the\nmodern synthesis\n• Bill Hamilton6 formulated theory of inclusive fitness and kin selection\n• Thomas Huxley7 \"Darwin's Bulldog\", early evolutionary biologist and science populariser\n• Lynn Margulis8 introduced the theory of eukaryotic cell origin through endosymbiosis\n• Barbara McClintock9 geneticist and molecular biologist, discovered transposons\n• Gregor Mendel10 discovered the basic rules of heredity\n• Ernst Mayr11 evolutionary biologist and science populariser\n• Mark Ridley12 science populariser\n• Fred Sanger13 founder of DNA and protein sequencing techniques"
  },
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    "chunk_id": 342,
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    "page": 173,
    "chunk_index_in_page": 1,
    "text": "scovered the basic rules of heredity\n• Ernst Mayr11 evolutionary biologist and science populariser\n• Mark Ridley12 science populariser\n• Fred Sanger13 founder of DNA and protein sequencing techniques\n• John Maynard Smith14 evolutionary biologist and science populariser\n• Alfred Russel Wallace15 evolutionary biologist\n• James Watson16 molecular biologist, discovered structure of DNA molecule\n• Edward Wilson17 founded \"sociobiology\"\nThis book is intended as a compilation of biographies describing the lives and work of\ninfluential biologists.\n1 http://en.wikipedia.org/wiki/Francis%20Crick\nhttp://en.wikibooks.org/wiki/General%20Biology%2FGallery%20of%20Biologists%2FCharles%\n2\n20Darwin\n3 http://en.wikipedia.org/wiki/Richard%20Dawkins\n4 http://en.wikipedia.org/wiki/Stephen%20Jay%20Gould\n5 http://en.wikipedia.org/wiki/J.B.S.%20Haldane\n6 http://en.wikipedia.org/wiki/William%20Hamilton\n7 http://en.wikipedia.org/wiki/Thomas%20Huxley\n8 http://en.wikipedia.org/wiki/Lynn%20Margulis"
  },
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    "text": "20Gould\n5 http://en.wikipedia.org/wiki/J.B.S.%20Haldane\n6 http://en.wikipedia.org/wiki/William%20Hamilton\n7 http://en.wikipedia.org/wiki/Thomas%20Huxley\n8 http://en.wikipedia.org/wiki/Lynn%20Margulis\n9 http://en.wikipedia.org/wiki/Barbara%20McClintock\n10 http://en.wikipedia.org/wiki/Gregor%20Mendel\n11 http://en.wikipedia.org/wiki/Ernst%20Mayr\n12 http://en.wikipedia.org/wiki/Mark%20Ridley\n13 http://en.wikipedia.org/wiki/Fred%20Sanger\n14 http://en.wikipedia.org/wiki/John%20Maynard%20Smith\n15 http://en.wikipedia.org/wiki/Alfred%20Russel%20Wallace\n16 http://en.wikipedia.org/wiki/James%20Watson\n17 http://en.wikipedia.org/wiki/Edward%20O.%20Wilson\n165"
  },
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    "page": 174,
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    "text": "Additional material\n33.1 External Links\n• EvoWiki: List of Biologists18\n18 http://wiki.cotch.net/index.php/List_of_biologists\n166"
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    "text": "34 Glossary\n• Autotroph1: an organism which can make its own energy\n• Cell2: Fundamental structural unit of all living things\n• Ether3:\n• Eukaryote4: an organism5 with a nucleus\n• Exoenzyme6: an enzyme used to break down organic molecules7 outside the body\n• Glycerol8:\n• Heterotroph9: an organism which can not make its own energy\n• Hydrocarbon10: an organic compound that contains carbon11 and hydrogen12 only.\n• Lipid13: fatty acid14 esters15 which form the basis of cell membranes\n• Nucleus16: Membrane17-bound organelle18 which contains the chromosomes19\n• Prokaryote20: an organism with no nucleus\n• Seed:\n• Flower:\n• Tracheid:\n• Haploid: A cell with a single set of chromosomes (23 in humans), in humans this is\nusually in gametes. This is commonly represented by n.\n• Diploid: A cell with two sets of chromosomes (46 in humans). This is commonly\nrepresented by 2n.\n• Sporangium:\n1 http://en.wikibooks.org/wiki/Autotroph\n2 http://en.wikibooks.org/wiki/Cell"
  },
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    "page": 175,
    "chunk_index_in_page": 1,
    "text": "ted by n.\n• Diploid: A cell with two sets of chromosomes (46 in humans). This is commonly\nrepresented by 2n.\n• Sporangium:\n1 http://en.wikibooks.org/wiki/Autotroph\n2 http://en.wikibooks.org/wiki/Cell\n3 http://en.wikibooks.org/wiki/Ether\n4 http://en.wikibooks.org/wiki/Eukaryote\n5 http://en.wikibooks.org/wiki/organism\n6 http://en.wikibooks.org/wiki/Exoenzyme\n7 http://en.wikibooks.org/wiki/organic%20molecule\n8 http://en.wikibooks.org/wiki/Glycerol\n9 http://en.wikibooks.org/wiki/Heterotroph\n10 http://en.wikibooks.org/wiki/Hydrocarbon\n11 http://en.wikibooks.org/wiki/Carbon\n12 http://en.wikibooks.org/wiki/Hydrogen\n13 http://en.wikibooks.org/wiki/Lipid\n14 http://en.wikibooks.org/wiki/fatty%20acid\n15 http://en.wikibooks.org/wiki/ester\n16 http://en.wikibooks.org/wiki/Cell%20nucleus\n17 http://en.wikibooks.org/wiki/Membrane\n18 http://en.wikibooks.org/wiki/organelle\n19 http://en.wikibooks.org/wiki/chromosome\n20 http://en.wikibooks.org/wiki/Prokaryote\n167"
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    "text": "Glossary\nThemajorityofthemodulesmakingupthisbookarebasedonnotesverygenerouslydonated\nby Paul Doerder, Ph.D.21 and Ralph Gibson, Ph.D.22 both currently of the Cleveland\nState University23.\nThe book was initiated by Karl Wick24, who donated many of his own class notes for other\nmodules, and who is fleshing out the outline format of Dr. Doerder's notes into text.\n34.1 Users\nAlsocal25\nDarren Hess26 MD/PhD recent grad, enjoys teaching, hopes to help work up the Nervous\nSystem Tissue section.\n21 http://bgesweb.artscipub.csuohio.edu/faculty/doerder.htm\n22 http://bgesweb.artscipub.csuohio.edu/faculty/gibson.htm\n23 http://www.csuohio.edu/\n24 http://en.wikibooks.org/wiki/User%3AKarl%20Wick\n25 http://en.wikibooks.org/wiki/User%3AAlsocal\n26 http://en.wikibooks.org/wiki/User%3Admhessmdphd\n168"
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    "text": "35 Contributors\nEdits User\n15 Adrignola1\n1 Alex.Szatmary2\n72 Alsocal3\n2 Arcanian Kastania4\n12 Avicennasis5\n1 Az15686\n1 Benlee7\n1 Bhatiajigar4068\n3 Bluelightstar9\n1 Blurpeace10\n2 Brother green11\n1 Cnelson12\n1 CommonsDelinker13\n1 Dallas127814\n1 DavidCary15\n10 Derbeth16\n2 Dets6517\n1 Dhs00118\n8 Dirk Hünniger19\n3 Dmhessmdphd20\n1 Dysprosia21\n1 http://en.wikibooks.org/w/index.php?title=User:Adrignola\n2 http://en.wikibooks.org/w/index.php?title=User:Alex.Szatmary\n3 http://en.wikibooks.org/w/index.php?title=User:Alsocal\n4 http://en.wikibooks.org/w/index.php?title=User:Arcanian_Kastania\n5 http://en.wikibooks.org/w/index.php?title=User:Avicennasis\n6 http://en.wikibooks.org/w/index.php?title=User:Az1568\n7 http://en.wikibooks.org/w/index.php?title=User:Benlee\n8 http://en.wikibooks.org/w/index.php?title=User:Bhatiajigar406\n9 http://en.wikibooks.org/w/index.php?title=User:Bluelightstar\n10 http://en.wikibooks.org/w/index.php?title=User:Blurpeace"
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    "text": "=User:Benlee\n8 http://en.wikibooks.org/w/index.php?title=User:Bhatiajigar406\n9 http://en.wikibooks.org/w/index.php?title=User:Bluelightstar\n10 http://en.wikibooks.org/w/index.php?title=User:Blurpeace\n11 http://en.wikibooks.org/w/index.php?title=User:Brother_green\n12 http://en.wikibooks.org/w/index.php?title=User:Cnelson\n13 http://en.wikibooks.org/w/index.php?title=User:CommonsDelinker\n14 http://en.wikibooks.org/w/index.php?title=User:Dallas1278\n15 http://en.wikibooks.org/w/index.php?title=User:DavidCary\n16 http://en.wikibooks.org/w/index.php?title=User:Derbeth\n17 http://en.wikibooks.org/w/index.php?title=User:Dets65\n18 http://en.wikibooks.org/w/index.php?title=User:Dhs001\n19 http://en.wikibooks.org/w/index.php?title=User:Dirk_H%C3%BCnniger\n20 http://en.wikibooks.org/w/index.php?title=User:Dmhessmdphd\n21 http://en.wikibooks.org/w/index.php?title=User:Dysprosia\n169"
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    "text": "Contributors\n1 Ec561822\n2 Ervinn23\n1 Fishpi24\n1 Gentgeen25\n5 Geocachernemesis26\n1 Greentea3627\n4 Guanabot28\n1 Hagindaz29\n1 Hanaa30\n5 Herbythyme31\n1 Iamunknown32\n6 Idraax33\n4 InfinityLiger34\n1 Italienmoose35\n2 Jaberwocky666936\n4 Jackaja37\n1 Javariel38\n1 Jclee39\n17 Jennrulez75740\n33 JetL01141\n19 Jguk42\n6 Jlee5278943\n35 Jomegat44\n2 Juadonsalazar45\n1 Kamran ahmad46\n22 http://en.wikibooks.org/w/index.php?title=User:Ec5618\n23 http://en.wikibooks.org/w/index.php?title=User:Ervinn\n24 http://en.wikibooks.org/w/index.php?title=User:Fishpi\n25 http://en.wikibooks.org/w/index.php?title=User:Gentgeen\n26 http://en.wikibooks.org/w/index.php?title=User:Geocachernemesis\n27 http://en.wikibooks.org/w/index.php?title=User:Greentea36\n28 http://en.wikibooks.org/w/index.php?title=User:Guanabot\n29 http://en.wikibooks.org/w/index.php?title=User:Hagindaz\n30 http://en.wikibooks.org/w/index.php?title=User:Hanaa\n31 http://en.wikibooks.org/w/index.php?title=User:Herbythyme"
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    "text": "php?title=User:Guanabot\n29 http://en.wikibooks.org/w/index.php?title=User:Hagindaz\n30 http://en.wikibooks.org/w/index.php?title=User:Hanaa\n31 http://en.wikibooks.org/w/index.php?title=User:Herbythyme\n32 http://en.wikibooks.org/w/index.php?title=User:Iamunknown\n33 http://en.wikibooks.org/w/index.php?title=User:Idraax\n34 http://en.wikibooks.org/w/index.php?title=User:InfinityLiger\n35 http://en.wikibooks.org/w/index.php?title=User:Italienmoose\n36 http://en.wikibooks.org/w/index.php?title=User:Jaberwocky6669\n37 http://en.wikibooks.org/w/index.php?title=User:Jackaja\n38 http://en.wikibooks.org/w/index.php?title=User:Javariel\n39 http://en.wikibooks.org/w/index.php?title=User:Jclee\n40 http://en.wikibooks.org/w/index.php?title=User:Jennrulez757\n41 http://en.wikibooks.org/w/index.php?title=User:JetL011\n42 http://en.wikibooks.org/w/index.php?title=User:Jguk\n43 http://en.wikibooks.org/w/index.php?title=User:Jlee52789\n44 http://en.wikibooks.org/w/index.php?title=User:Jomegat"
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    "text": "dex.php?title=User:JetL011\n42 http://en.wikibooks.org/w/index.php?title=User:Jguk\n43 http://en.wikibooks.org/w/index.php?title=User:Jlee52789\n44 http://en.wikibooks.org/w/index.php?title=User:Jomegat\n45 http://en.wikibooks.org/w/index.php?title=User:Juadonsalazar\n46 http://en.wikibooks.org/w/index.php?title=User:Kamran_ahmad\n170"
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    "text": "Users\n179 Karl Wick47\n1 Karthik48\n1 Kksf197949\n1 Kotireddyanekallu50\n12 Lazyquasar51\n2 Lexor52\n3 Liblamb53\n1 Ltellez54\n1 MarkHudson55\n4 Marshman56\n1 Mathonius57\n4 Mattb11288558\n1 Mh7kJ59\n7 Mike.lifeguard60\n9 Moadeeb61\n7 Monk62\n1 Naryathegreat63\n2 Neoptolemus64\n1 NipplesMeCool65\n1 Nmontague66\n2 Obscureownership67\n4 Panic2k468\n1 Perl69\n1 Petemella70\n16 QuiteUnusual71\n47 http://en.wikibooks.org/w/index.php?title=User:Karl_Wick\n48 http://en.wikibooks.org/w/index.php?title=User:Karthik\n49 http://en.wikibooks.org/w/index.php?title=User:Kksf1979\n50 http://en.wikibooks.org/w/index.php?title=User:Kotireddyanekallu\n51 http://en.wikibooks.org/w/index.php?title=User:Lazyquasar\n52 http://en.wikibooks.org/w/index.php?title=User:Lexor\n53 http://en.wikibooks.org/w/index.php?title=User:Liblamb\n54 http://en.wikibooks.org/w/index.php?title=User:Ltellez\n55 http://en.wikibooks.org/w/index.php?title=User:MarkHudson\n56 http://en.wikibooks.org/w/index.php?title=User:Marshman"
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    "text": "Contributors\n1 Ravichandar8472\n16 Recent Runes73\n2 Robert Horning74\n1 Rymwoo75\n1 SB Johnny76\n2 SMH77\n32 Sam Stultus78\n3 Savh79\n1 Shaggyjacobs80\n2 Silkiesttie81\n2 Smellyone82\n1 Some P. Erson83\n1 Starwindfury84\n3 Steinsky85\n2 Swift86\n1 T.D. Migneault87\n2 TUF-KAT88\n1 Tannin89\n12 Taoster90\n1 Teaandcrumpets91\n13 Thenub31492\n1 Theornamentalist93\n15 Toriber94\n5 Uncle G95\n1 Webaware96\n72 http://en.wikibooks.org/w/index.php?title=User:Ravichandar84\n73 http://en.wikibooks.org/w/index.php?title=User:Recent_Runes\n74 http://en.wikibooks.org/w/index.php?title=User:Robert_Horning\n75 http://en.wikibooks.org/w/index.php?title=User:Rymwoo\n76 http://en.wikibooks.org/w/index.php?title=User:SB_Johnny\n77 http://en.wikibooks.org/w/index.php?title=User:SMH\n78 http://en.wikibooks.org/w/index.php?title=User:Sam_Stultus\n79 http://en.wikibooks.org/w/index.php?title=User:Savh\n80 http://en.wikibooks.org/w/index.php?title=User:Shaggyjacobs\n81 http://en.wikibooks.org/w/index.php?title=User:Silkiesttie"
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    "text": "Teaandcrumpets\n92 http://en.wikibooks.org/w/index.php?title=User:Thenub314\n93 http://en.wikibooks.org/w/index.php?title=User:Theornamentalist\n94 http://en.wikibooks.org/w/index.php?title=User:Toriber\n95 http://en.wikibooks.org/w/index.php?title=User:Uncle_G\n96 http://en.wikibooks.org/w/index.php?title=User:Webaware\n172"
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    "text": "List of Figures\n• GFDL:GnuFree DocumentationLicense. http://www.gnu.org/licenses/fdl.html\n• cc-by-sa-3.0: Creative Commons Attribution ShareAlike 3.0 License. http://\ncreativecommons.org/licenses/by-sa/3.0/\n• cc-by-sa-2.5: Creative Commons Attribution ShareAlike 2.5 License. http://\ncreativecommons.org/licenses/by-sa/2.5/\n• cc-by-sa-2.0: Creative Commons Attribution ShareAlike 2.0 License. http://\ncreativecommons.org/licenses/by-sa/2.0/\n• cc-by-sa-1.0: Creative Commons Attribution ShareAlike 1.0 License. http://\ncreativecommons.org/licenses/by-sa/1.0/\n• cc-by-2.0: Creative Commons Attribution 2.0 License. http://creativecommons.\norg/licenses/by/2.0/\n• cc-by-2.0: Creative Commons Attribution 2.0 License. http://creativecommons.\norg/licenses/by/2.0/deed.en\n• cc-by-2.5: Creative Commons Attribution 2.5 License. http://creativecommons.\norg/licenses/by/2.5/deed.en\n• cc-by-3.0: Creative Commons Attribution 3.0 License. http://creativecommons.\norg/licenses/by/3.0/deed.en"
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    "page": 183,
    "chunk_index_in_page": 1,
    "text": "reative Commons Attribution 2.5 License. http://creativecommons.\norg/licenses/by/2.5/deed.en\n• cc-by-3.0: Creative Commons Attribution 3.0 License. http://creativecommons.\norg/licenses/by/3.0/deed.en\n• GPL: GNU General Public License. http://www.gnu.org/licenses/gpl-2.0.txt\n• LGPL: GNU Lesser General Public License. http://www.gnu.org/licenses/lgpl.\nhtml\n• PD: This image is in the public domain.\n• ATTR: The copyright holder of this file allows anyone to use it for any purpose,\nprovided that the copyright holder is properly attributed. Redistribution, derivative\nwork, commercial use, and all other use is permitted.\n• EURO: This is the common (reverse) face of a euro coin. The copyright on the design\nof the common face of the euro coins belongs to the European Commission. Authorised\nis reproduction in a format without relief (drawings, paintings, films) provided they\nare not detrimental to the image of the euro.\n• LFK: Lizenz Freie Kunst. http://artlibre.org/licence/lal/de"
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    "source_file": "GeneralBiology.pdf",
    "page": 183,
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    "text": "rised\nis reproduction in a format without relief (drawings, paintings, films) provided they\nare not detrimental to the image of the euro.\n• LFK: Lizenz Freie Kunst. http://artlibre.org/licence/lal/de\n• CFR: Copyright free use.\n175"
  },
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    "chunk_id": 363,
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    "page": 184,
    "chunk_index_in_page": 0,
    "text": "List of Figures\n• EPL: Eclipse Public License. http://www.eclipse.org/org/documents/epl-v10.\nphp\nCopies of the GPL, the LGPL as well as a GFDL are included in chapter Licenses101. Please\nnote that images in the public domain do not require attribution. You may click on the\nimage numbers in the following table to open the webpage of the images in your webbrower.\n101 Chapter 36 on page 179\n176"
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    "text": "List of Figures\n1 GFDL\n2 User:102 PD\n3 Unknown, The Hornet is no longer in publication and it is PD\nverylikelyfora20-year-oldartistin1871tohavediedbefore\n1939\n4 PD\n5 GFDL\n6 GFDL\n7 PD\n8 Uploader, CDC GFDL\n9 LadyofHats103 PD\n102 http://en.wikibooks.org/wiki/User%3A\n103 http://en.wikibooks.org/wiki/User%3ALadyofHats\n177"
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    "text": "36 Licenses\n36.1 GNU GENERAL PUBLIC LICENSE\nVersion3,29June2007 network,withnotransferofacopy,isnotconvey- Youmaychargeanypriceornopriceforeachcopy Ifyouconveyanobjectcodeworkunderthissec-\ning. thatyouconvey,andyoumayoffersupportorwar- tionin,orwith,orspecificallyforusein,aUser\nCopyright © 2007 Free Software Foundation, Inc. rantyprotectionforafee. 5. ConveyingModified Product, and the conveying occurs as part of a\n<http://fsf.org/> Aninteractiveuserinterfacedisplays“Appropriate SourceVersions. transaction in which the right of possession and\nLegalNotices”totheextentthatitincludesacon- useoftheUserProductistransferredtothere-\nE t it i v m i e s r c y n o o o p n t i e e a s i l s lo o p w f e e t r d h m ."
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    "text": "which the right of possession and\nLegalNotices”totheextentthatitincludesacon- useoftheUserProductistransferredtothere-\nE t it i v m i e s r c y n o o o p n t i e e a s i l s lo o p w f e e t r d h m . is it P t l r i e c e d e a n t m o s b e c l o e d p o y cu a m nd en d t i , st b r u ib t u c t h e a v n e g r i b n a g - v p t c h e e la p n e y t i u e s n s t a e o t n r a t t n a h h p d e a p p t r e r o t x o h p t m e e ri r n i a e n t t e i e t n s h c t n l o a y o p t y v w w r i a s i a g i r r b r h r a l t a e n n n f t t e o y i a t e f i t s o c u e r r a , e t r a h e t n e h p d a w r t ( o o 2 ( v r 1 ) i k d ) t ( e e d e d l i x l s ) s - - , Y t i t n h i o o e u n th m 4 m e , o a f d p y o i r r fi o c m v c o a i n d o t v i f e e o d s y n o t s u a h t r a o w c t e o p y r c r o k o o u d d b a e u a l c s s u e e o n d i m d t o e e r f n e r t o t t h m a h e l e l t t o P h e f e r r m o t P h g s r e r a o s o e m g f r c , s a o e m o n c r - - , c"
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    "text": "w c t e o p y r c r o k o o u d d b a e u a l c s s u e e o n d i m d t o e e r f n e r t o t t h m a h e l e l t t o P h e f e r r m o t P h g s r e r a o s o e m g f r c , s a o e m o n c r - - , c l C m e i o p s u s r i s e r t e o n s f b t p e h o in o n a w d c p c in e o t r g m h p e p e S t a o t u n r u i a i r t e n c y d s e a o b c c r o y ti n f o t o v n h r e e y i a e s I d n fi c s h u x t a n a e r d d ll a e a c t r t t e i e t o r r h m n i i z s I e ( n d s r f e ) e o c , g r t a m t i r o h d a n e - -\nT T l c t G t o f u s t p i o o e h o a f s r c h h N r e f l i o e e a e e t s s g U n a w w t y h r p G l s w h o l a a o l a e i G r e u a N r r c r m o i e y e k f t e r e G g U o ; s s n n s r , f r N a b s i e a u r G a t n y e t r e U s m s r o s a d o e e a e e i l – o d n f r p G t t f t . c s o P s e d p o w o e h ."
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    "text": "e i G r e u a N r r c r m o i e y e k f t e r e G g U o ; s s n n s r , f r N a b s i e a u r G a t n y e t r e U s m s r o s a d o e e a e e i l – o d n f r p G t t f t . c s o P s e d p o w o e h . r m e r l u n a a a a i s W m b e e u r l n i m s t e g l r t a g e P i o a n h c o k , a e a u l e o s e l s t n L b P s d t r t h h d o s s i h l u a e c i u . t s e c b t e r o o o r F o e n l t Y e L f w i r h t s t c o a e i a i w o e a e c t u e n n L r r k e a i y k d r i e n S s r c k c e s e s o a o e i i m . c a e n n f n t n h w t a h t a d i s w a B e n a s i a e e s n n n a y y d r p a f g o s r d p o w e e y f c e f o f r l r o o d o r y w F t a e m e u n r h o e l o e t k i r t l e o , u t o r r r s s k v n r f a c t o g t r e s e o s d o p e f u l . t r o p t a e e r , s a w f y y a t d a i r i o l o o s t a c o a o e h e n u u t r m n n f d i e e s r r t - - , “ A T w t c t o l f t s i o O h h h t e p s o h a r n a e e t “ t b r m e n r s t i S k j m o e i d e “ ."
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    "text": "i h r e e o r e Y s n y n r c y o f i s t d t o t t w w i h p t a h p o i u o i h h i r g n r n s t o a n c i i o o m h v s m o n L l t m s e e i u p y o 7 i L n e y i i c y s . n c o g n i a e t l . a c t e f i e p n i e c r n a T l n o T t p s e n e i t h t n e c h n l r s h p i e e e n e i n s c t i n a s 4 l s e o o a o w e c a s t b t v r k L t e t o n a i i e a l o h c a c r n i d e q t n c e k e e g y h “ u e s t s s e , a o k e n e w i d n n s s a d r c e s . o t t e y n e e t a e e a a r m i n p d t T o k w t t c w e t i i e n h o i . a h n n i n i r i n n i l l n o g g 7 e s t * l l - - T w y v t m a t p c m d a a i i i o i m d c r e o h o o p o o o o r u n v r n n e l i p d d o v k e i a e ."
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    "text": "t T o k w t t c w e t i i e n h o i . a h n n i n i r i n n i l l n o g g 7 e s t * l l - - T w y v t m a t p c m d a a i i i o i m d c r e o h o o p o o o o r u n v r n n e l i p d d o v k e i a e . n e s l i i i r n t d e fi fi r d s d o s t B e t e , o e e e e h r s , t q u e w t d d l a h a o y u s s h t t t h e u n r h i o o e t n r e p y a h e r f b n h e n o w o ff p a m j e i t r i t r e s s o o e n h t t u c e w c t r r i h s i r l b t n n h t k r t e t e e o e d s c t a e s q s c r e h l m l u e k o u p U t a n l t a r e i . h d d a n o o s r s v d m e e r e d e d e i ."
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    "text": "thisLicensetoapplytotheotherpartsofthe ProgramremainsgovernedbythisLicensewithout\ngram,whethergratisorforafee,youmustpass The“CorrespondingSource”foraworkinobject aggregate.6.ConveyingNon-SourceForms. regardtotheadditionalpermissions.\nontotherecipientsthesamefreedomsthatyoure- codeformmeansallthesourcecodeneededtogen-\nc o th e r i e v c m e a d n t . h g Y e e s o t e u t t m e h r e u m s s t s o m u so r a c t k e h e e c s y o u d r k e e n . o t w h A a n t t h d t e h i y r e o y r u , ig t m o ht o u s , s . r t ec sh ei o v w e e t s h c ra r e i t p e o t , b s j i e t n o c s t t c a c o l o n l d , tr e o a a l n n d th d o ( t s f o o e r m ac a o t n d iv i i f e t y x ie e t s c h ."
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    "text": "t l . o p r ( k A e , r d m y d o i i u s t s io m io n a n a y s l\nnotincludethework’sSystemLibraries,orgeneral- ingSourceunderthetermsofthisLicense,inone permissionsmaybewrittentorequiretheirownre-\nDevelopers that use the GNU GPL protect your purposetoolsorgenerallyavailablefreeprograms oftheseways: movalincertaincaseswhenyoumodifythework.)\nrightswithtwosteps: (1)assertcopyrightonthe whichareusedunmodifiedinperformingthoseac- Youmayplaceadditionalpermissionsonmaterial,\nsoftware,and(2)offeryouthisLicensegivingyou tivitiesbutwhicharenotpartofthework. For * a) Convey the object code in, or embodied in, addedbyyoutoacoveredwork,forwhichyouhave\nlegalpermissiontocopy,distributeand/ormodify example,CorrespondingSourceincludesinterface aphysicalproduct(includingaphysicaldistribu- orcangiveappropriatecopyrightpermission.\nit. definitionfilesassociatedwithsourcefilesforthe tionmedium),accompaniedbytheCorresponding"
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    "text": "rceincludesinterface aphysicalproduct(includingaphysicaldistribu- orcangiveappropriatecopyrightpermission.\nit. definitionfilesassociatedwithsourcefilesforthe tionmedium),accompaniedbytheCorresponding\nF G t s h a o P k i r s e L , t f h c r t l e e h e e e a d r s G e l o y v P f e t e l L w x o a p p r r l e e a e r q . i s n u ’ s ir F a e t o n h s r d a t t b h a o a t u h t t t h e h m r o e u o r s s i d s e ’ i r fi n s p e ’ o r d o a w t n v e a d e c r r t r s i a a o i n o u n t n t , y h s o t f b h r o s e e r ’ w d s d s p u y a o b e t n r c a p k a i r , m fi c o a o c i g c a n m r a l d a l m l y m l t y u h d s n e e l a i i s c n n s i a g o k d t n u e i d o e o r d c t n h e s t u e o o c r r b o r p p c d e r o a e q o n r u g t f t i o r s r r a r o e o m l , s f h s fl s t u a o h t c r w e h h e a d w b a t s o e li t r t b b w k h y r ."
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    "text": "n u e i d o e o r d c t n h e s t u e o o c r r b o r p p c d e r o a e q o n r u g t f t i o r s r r a r o e o m l , s f h s fl s t u a o h t c r w e h h e a d w b a t s o e li t r t b b w k h y r . e e a i e r n w n i t e o i s t m r h k a o a n s t i d e e s ( S a o p i r b o a n i u n j c l e y l r i c u e c u t d d e s i c fi e n b o d g x y d e f e a o d a r i p o n w s h n , o r y f i o a s t t r w i t c d e e a a n u m r l r e a o b d i b ff o i n s l d e t t e r e i r e , p i r b d c h v h u y a i a t n s l i n i i , o d c g n a a e f l ."
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    "text": "f e a o d a r i p o n w s h n , o r y f i o a s t t r w i t c d e e a a n u m r l r e a o b d i b ff o i n s l d e t t e r e i r e , p i r b d c h v h u y a i a t n s l i n i i , o d c g n a a e f l . m o p m r * h e e y d a b d s i t ) i u i c u C m l a e m o l a ) n , s p c v t a r u e o c s t y c d t h o o t u r h m m e c e e t - - N c m m te e o a a r n t m y t s w e e s ( r i , : i i t f a f h o l a s ) r t u s a t m u n h p a d o p t i r e n i l z e r g i e m a d l a en n b y t y y ou t t h o h a e t e d h t d c e e o r r t p m o y p s r r a i o o g v f c h o i t t s v h i e o h is r n o e L l d d i o e c w f r e s o n t r s o h k e f i , s w t y h i L o t a u h i t -\nmarkedaschanged,sothattheirproblemswillnot yearsandvalidforaslongasyouofferspareparts\nbe attributed erroneously to authors of previous The Corresponding Source need not include any- or customer support for that product model, to\nversions."
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    "text": "lnot yearsandvalidforaslongasyouofferspareparts\nbe attributed erroneously to authors of previous The Corresponding Source need not include any- or customer support for that product model, to\nversions. thingthatuserscanregenerateautomaticallyfrom giveanyonewhopossessestheobjectcodeeither *a)Disclaimingwarrantyorlimitingliabilitydif-\notherpartsoftheCorrespondingSource. (1)acopyoftheCorrespondingSourceforallthe ferentlyfromthetermsofsections15and16ofthis\nT T w S i s o a p h l r f t n e u e h i f r o r i e h h d m s b a t e e e m p i e t e u a d c i s h s a r t f r i e y s r o a s l t e a o y i l t e e v t h s d r t f h e s e l e o v e i o e y t d e c s f m r e p v e e t u o d e r w m p r i i , r m n x s e c n s o r u h i s e a d t u g d a o a n i e e s t a b o c g n u l n r i u t m f t s n c a s c e m d h s i t t r e u c e e a p o i s o o e d e s t n r t n u a f d e h s t t d f t g f i ’ r t i a i o i o s t t fi e h s s h a f l h e r r ."
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    "text": "a n i e e s t a b o c g n u l n r i u t m f t s n c a s c e m d h s i t t r e u c e e a p o i s o o e d e s t n r t n u a f d e h s t t d f t g f i ’ r t i a i o i o s t t fi e h s s h a f l h e r r . s l r e m i l r p y e i s e l d t t n g i y r e o h n h n o G v d i s v o e d i o n e v e t n o e P f s i d c r i m v r e m s u s o s L o s i i i u t n m t d i o p a , o t o o h c a n u n n r o p n h a c e o u a d a s s c r t c d o l f a e t o e h s a u f d o n i b n p a b c f c o t y u e t t t t n l h t m o e a h s e u t s g u o d e h b e r . a e s s u e w e e l i o e e e d I G r t s n i c r f . s h e t s d s c P o , c h t e s , T o u f a o u L a w t m w s r h n c t c w o s e p e h h h c t a f a r o i r e d e t i i s n e r p c o n w s t o e f h s t p r a a s o a t e o n i r i h r s r t i c m b n i o e o n d e o e s t - - - , . ."
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    "text": "u f a o u L a w t m w s r h n c t c w o s e p e h h h c t a f a r o i r e d e t i i s n e r p c o n w s t o e f h s t p r a a s o a t e o n i r i h r s r t i c m b n i o e o n d e o e s t - - - , . . A T T y v f f i m p L s r o o t o i u i h h l r d i i r r c u l e t s t m e i e e u s s r v t r d n f i C h o t i r o L r s i g e e o c o s b n i e s i h a g m r y c t t t b r h a o t e e h s e t o l c n n r r e a s c s o u m s l g p o t r y p e n p r o v o u y a s n r f o e n n i e a r o n f i r f x d f i n m v t e g a t p c i t e g d i n h h i e h o d l d r i g e t a p e w e c w d u y i u S l o u c o t o a r s n o r o l n u t r w i e y k d u v g h k m t . . e h e r . o p e a c o r r t r T u ffi 2 e e s d t d o t t . h o i f , r a h n fi o t i m B w s t i h g r e s e t a i o e d s L a d h v s r r L i e e i y k w c P c c i n e o e c o o P r q i u n P e o s n r i u r n r s t k g e d o c i e s s r r v i u g o i e m a t a a n v r c n i m c l a o o e i a l e s k s i m r n n ."
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    "text": "e d s L a d h v s r r L i e e i y k w c P c c i n e o e c o o P r q i u n P e o s n r i u r n r s t k g e d o c i e s s r r v i u g o i e m a t a a n v r c n i m c l a o o e i a l e s k s i m r n n . r n o m s n e e t s u i t , d o e o T i , r a t w n g a n c h b e a r r n t s e l d e y e s a , e . d c n d m c t o p p o t g a h o u r e e d e e r n i o r t d t e e s s - - - - . s c u t t C c c t l o f o p a o e h h h o h e o n b c s l o w r a n f a i e c e a d l j , r t s y c e e d s n e r e w r e i s c C e g d e c n i s a t , y f e f s w o o ( o r ."
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    "text": "c a n a i e 1 a c h o i s n 9 u b v n n e W 9 m l e o e e 6 w i I l ff v s , a o l P i e a e n g t e o O n w c h f y i r - - - - A w u h s m d a t c t i h o o g c o o h c i l m e t e u u n “ u d i ” . c U s b i l m s , h n a e t t f s h r g f o o F w a e u o n r i t o r u h s l w l u r d s i u P i s c h c e n n a s h a r r e c p o e o o , s t o f u r p e m h d “ o r m s r a e u t p n f e p r r h a c o o a s t t o e t l h r r n h i a l s ” c m a y a s e a p u t l s p t i a a l i a l s , o u r a l r n c l o b n s r t e y o l y d e i e a i r c d t p u s i u u t h n r s r c s a ( l e e t o t e 2 f a n o s o r o d d ) r o g f i r u ” s l ( i a p u v a b c 1 r p r e a s n t l ) e d o e e d e y f r w r d a c r t e p e s o i u h r e o n o c e “ n s c i l r e n r n c l s t i i s t f o a u , g n v o a o o n l m e g v f r n , s d d e a ."
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    "text": "arties’legalrightstoforbid ucthassubstantialcommercial,industrialornon- thenyourlicensefromaparticularcopyrightholder\nTo“propagate”aworkmeanstodoanythingwithit circumventionoftechnologicalmeasures. 4. Con- consumeruses,unlesssuchusesrepresenttheonly isreinstated(a)provisionally,unlessanduntilthe\nthat,withoutpermission,wouldmakeyoudirectly veyingVerbatimCopies. significantmodeofuseoftheproduct. copyrightholderexplicitlyandfinallyterminates\norsecondarilyliableforinfringementunderappli- yourlicense,and(b)permanently,ifthecopyright\ncablecopyrightlaw,exceptexecutingitonacom- YoumayconveyverbatimcopiesoftheProgram’s “Installation Information” for a User Product holderfailstonotifyyouoftheviolationbysome\nputerormodifyingaprivatecopy.Propagationin- sourcecodeasyoureceiveit,inanymedium,pro- means any methods, procedures, authorization reasonablemeanspriorto60daysafterthecessa-"
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    "text": "t D i t o a e o n i s n c s u \" X E m X Y n e Y t Z n i Z t tl i w e i n n d h a o p X n s a e Y o r t e t Z h n i \" t e t l r h e m e l e s e a i e a t n s n h g s e f u o r a a l i l g s o n e w p . a i r m n e ( g c e H i d s t e e e r s l x e u y t b X X t u h Y Y n a i Z Z t t l c I i f o s v t y e e o d r u ,a ( p a n u s d b m l c i o s a h n n t y i o n r u a d e s i t s fi h t t r e ib r r e u e a s t t s e o o n O n a p t b o a l q y a u ) d e j o a c n c o e p n t i h t e e s pa a o g c f e t t s u h . a e l\nSectionsthentherearenone. standsforaspecificsectionnamementionedbelow, Documentnumberingmorethan100,youmustei-\nThisLicenseisakindof\"copyleft\",whichmeans such as \"Acknowledgements\", \"Dedications\", \"En- therincludeamachine-readableTransparentcopy\nt s t le h h e f l a e t v t e G l s i d c N e e b r U n e i s v e G a fr t d e e i e n v es e e i i r g n w a n l o t e r h P d k e u s f b o s o l r a i f m c f t r e L h ee e i s c e s e d n o n o f s s c t e e w u ."
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    "text": "a e e e g o e n n t h h u s s f n h q n n t h s a t e e e n h s t u e o o e i m r i e d s e . f i t r v n p p n r r i e e n t e * r u e u c t o r t h e o c d e h b o b t h i I q e o t . t i e f t l . l e c i s u C i p i h D c * s P c t e c i A y T e e o h h r o o r H r v e f d p e e i p e t c i o t m t e r . d g h e s u y e r l p r . e r I h e e e m r r e n m u r n , t y i m T n * f v g c b e d o u a t i e n e l h s n s l u . u n u x D l i o s t t l t s r m t d d o i * . t . h h l s o n e i f i m e e a * c n P s C o b g a r e d t t t o r s E e i . s n s h t i d v e e d o l . c . o S i o s c e o f u i e s t A e w t t n fi f * s n o u t a r i , c d I L . o h a v s t i n F a i d n n a i l e e e e t * - - - - . Y n n d I m d p o u S t c N i l f o a o e r m e o c a e o fi c t m r G u e t i n e v t s m , h n t n i e e i b m o e e s D d a m s t e y d n s n e r a r O I e , s s f d e d n y o t n ."
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    "text": "n d v n h y t n t h d e e D l i \" o e t o i t \" e o r , s s t w o A t f s n S e i ( h i c c L e c t o e s t u a o e e I k h e h c i n t n m s c n f n c t i e e v s i t o t a w y e o n t a i h w n L n o o r h n i r s i e l d u n t i l i e e s s l - - - - , \" \" \" A w v t a t s l C c M M C i h h i o i n s o t t r d a o r C h t e e r a M e p t r e r k e a s - s m i x o d C B s t s b C p r a i i . p e u Y v v a o u m o r a S e e t t n - o b l n i i p i S l A o m o l t a s l t C i A n e n e b s h M i a \" - o h n \" p o e ) S n o m w u e e u r y h f s M n a l b m i m t a t t t s m s l i M c r h i e i u e a o o f c e o a e t c a u n n C p a n a h c t s o \" w A y n s i h f s l r s a p i l o i ( C i k i c i a t t r o r g k o i i o s n e i r h e e n e p r . y t s t t r p c y \" h C a h v 3 i f M o r W e p b o e a o . i r 0 g r a l r t M l a o e ."
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    "text": "c t s o \" w A y n s i h f s l r s a p i l o i ( C i k i c i a t t r o r g k o i i o s n e i r h e e n e p r . y t s t t r p c y \" h C a h v 3 i f M o r W e p b o e a o . i r 0 g r a l r t M l a o e . l h l t a a r C t l a i C l b n p w A i o a d n c \" y o r l n b o y e ) a e b r , \" l r n W b c a a e M o k c s e o t t o a d s e w i i i d a d v n o y o o s y a e e n t n p f s r t a n i o u k o i v c W b d t n s b a e u S - e C e l e n f t d i s a i d o M b h o s t i l i r h n e u m s t e - u i \" o e e s s d p n t m l e d s i t h r p s r t p i o o t o v ( u a r b h fi n o s i e u b i o n y e e s s r r t - - -\na a th n n e d it T p e i m u t b le s li t P s a h a t e i g n r e g ."
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    "text": "u so c t w e h d c i e a th l b L l y e i w d b c r h o a t i h m c r h y e - . t d c r s o h a m o r e m e r r a f p e e l L t o w l t e i r e r e b m a r m r r t s a a e , l s c r i d n r d y o o . e m a f s s t , Y a y a i t o o n i e n s u u r t l l r i e r i m a n u n c l e c g a h i t t y o s f u h u i r c c n ) n e , o e o c , n y t l t v a o i p l o e y u i r m y n o o d s u v i s o t t i u a d e s c n b d e h a d d o t n t o o h d t t b e h n o m j a a u e f c t c p m , c t t l e h a e i s c f e r t s o i e o t c f d s o h r a e s l e l ( l , t o u p i e w o n n a n r - - - - I q o i m b n n f y u o f f i t o o d r r h r r e i e m e m fi d c e o a G a t d m t t o N i i o b o v p U n n i e r n r , o G i s i v n b s i P o i g u d n n L t e o e , o o c r s a n f e u n r l s c t y e s d h h a li i e r o n f i y n n k y C f l i o y o t n o u o r m g t m o w b i t a n o i h t t n s u h e i t e o l e a d d n A l e l o p W x u a t p t n h o n e l d i e r n d c e k r t a r w e t t p s"
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