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Contents

1 Getting Started 3

2 Biology - The Life Science 5 2.1 Characteristics of life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2 Nature of science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3 Scientific method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.4 Charles Darwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.5 After Darwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.6 Challenges to Darwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

3 The Nature of Molecules 11 3.1 Matter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3.2 The atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3.3 Mass and isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 3.4 Electrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 3.5 Chemical bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.6 Chemical reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.7 Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

4 The Chemical Building Blocks of Life 15 4.1 Carbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 4.2 Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 4.3 Stereoisomers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 4.4 Lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 4.5 Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 4.6 Hereditary (Genetic) information . . . . . . . . . . . . . . . . . . . . . . . 18

5 Life: History and Origin 19 5.1 Properties of life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 5.2 Origin of life: 3 hypotheses . . . . . . . . . . . . . . . . . . . . . . . . . . 19 5.3 The early earth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 5.4 Origin of cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 5.5 The RNA world? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 5.6 The earliest cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 5.7 Major steps in evolution of life . . . . . . . . . . . . . . . . . . . . . . . . 22

6 Cells 23

7 Cell structure 25 7.1 What is a cell? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 7.2 History of cell knowledge . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

III

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7.3 Microscopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 7.4 Cell size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

8 Structure of Eukaryotic cells 31 8.1 Structure of the nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 8.2 Chromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 8.3 Endoplasmic reticulum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 8.4 The Golgi apparatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 8.5 Ribosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 8.6 DNA-containing organelles . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 8.7 Cytoskeleton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

9 Membranes 37 9.1 Biological membranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 9.2 Phospholipid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 9.3 Fluid mosaic model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 9.4 Membrane proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 9.5 Receptor-mediated endocytosis . . . . . . . . . . . . . . . . . . . . . . . . 40

10 Cell-cell interactions 41 10.1 Cell signaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 10.2 Communicating junctions . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

11 Energy and Metabolism 43 11.1 Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 11.2 Oxidation–Reduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 11.3 NAD+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 11.4 Free energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 11.5 Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 11.6 ATP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 11.7 Biochemical pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

12 Respiration: harvesting of energy 47 12.1 Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 12.2 Respiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 12.3 Respiration of glucose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 12.4 Alternative anaerobic respiration . . . . . . . . . . . . . . . . . . . . . . . 47 12.5 Glycolysis overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 12.6 Regeneration of NAD+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 12.7 Alcohol fermentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 12.8 Lactate formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 12.9 Krebs cycle: overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 12.10 ATP production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 12.11 Evolution of aerobic respiration . . . . . . . . . . . . . . . . . . . . . . . . 49

13 Photosynthesis 51 13.1 Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 13.2 “Dark” reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 13.3 Prokaryote cell division . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Contents

13.4 Bacterial DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 13.5 Chromosome number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 13.6 Eukaryotic chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 13.7 Chromosome organization . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 13.8 Human karyotype stained by chromosome painting . . . . . . . . . . . . . 55 13.9 Chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 13.10 Human chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 13.11 Mitotic cell cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 13.12 Replicated human chromosomes . . . . . . . . . . . . . . . . . . . . . . . . 56 13.13 Mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 13.14 Plant mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 13.15 Controlling the cell cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 13.16 Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 13.17 Mutations and cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

14 Sexual reproduction 59 14.1 Sexual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 14.2 Sexual life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 14.3 Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 14.4 Prophase I: synapsis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 14.5 Crossing over . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 14.6 Microtubules and anaphase I . . . . . . . . . . . . . . . . . . . . . . . . . 60 14.7 Meiosis II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 14.8 Evolution of sex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 14.9 Consequences of sex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

15 Genetics 63

16 Gregor Mendel and biological inheritance 65 16.1 Mendel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 16.2 Mendel’s experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 16.3 Mendel’s seven pairs of traits . . . . . . . . . . . . . . . . . . . . . . . . . 66 16.4 Locus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 16.5 Modern Y chromosome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 16.6 Chromosome phenomena . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 16.7 X-chromosome inactivation . . . . . . . . . . . . . . . . . . . . . . . . . . 67 16.8 Barr body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 16.9 Human genetic disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

17 DNA: The Genetic Material 69 17.1 DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 17.2 Historical perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 17.3 Hershey-Chase Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . 69 17.4 DNA/RNA components . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 17.5 Chemical structure of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . 70 17.6 3D structure of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 17.7 Franklin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 17.8 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Contents

17.9 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 17.10 DNA polymerases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 17.11 DNA replication complex . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 17.12 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 17.13 DNA replication fork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 17.14 Replication units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 17.15 Replicon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 17.16 What is gene? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

18 Gene expression 75 18.1 “Central Dogma” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 18.2 The Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 18.3 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 18.4 Transcription bubble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 18.5 Eukaryote mRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 18.6 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 18.7 Translation in bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 18.8 Aminoacyl tRNA synthase . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 18.9 Ribosome structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 18.10 Large ribosome subunit . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 18.11 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 18.12 Initiation complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 18.13 Elongation, translocation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 18.14 Introns/exons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

19 Gene regulation 79 19.1 Transcriptional control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 19.2 DNA grooves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 19.3 Regulatory proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 19.4 Lac operon of E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 19.5 Alternative splicing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

20 Mutation 81 20.1 Point Mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 20.2 Substitution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 20.3 Larger mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 20.4 Chromosomal mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 20.5 Causes of mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 20.6 Effects of mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 20.7 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 20.8 Original notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 20.9 Point mutation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 20.10 Acquisition of genetic variability . . . . . . . . . . . . . . . . . . . . . . . 84 20.11 Eukaryote genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 20.12 Barbara McClintock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

21 Recombinant DNA technology 87 21.1 Recombinant DNA technology . . . . . . . . . . . . . . . . . . . . . . . . . 87

Contents

21.2 Restriction endonucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 21.3 Restriction endonucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 21.4 Uses of cloned gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 21.5 Other molecular procedures . . . . . . . . . . . . . . . . . . . . . . . . . . 88 21.6 RFLP(restriction fragment length polymorphism) analysis . . . . . . . . . 89 21.7 Sanger DNA sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 21.8 Automated sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 21.9 Genome projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 21.10 Biochips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 21.11 DNA chip controversies . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 21.12 Gene patenting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 21.13 Stem cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

22 Classification of Living Things 93 22.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 22.2 Viral Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 22.3 Viral Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 22.4 Viruses Practice Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 22.5 Archaea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 22.6 Prokaryote evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 22.7 Domains of life: characteristics . . . . . . . . . . . . . . . . . . . . . . . . 101 22.8 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 22.9 Classification of Protists . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 22.10 Protozoa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 22.11 Algae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102 22.12 Slime molds & Water molds . . . . . . . . . . . . . . . . . . . . . . . . . . 103 22.13 Protists Practice Questions . . . . . . . . . . . . . . . . . . . . . . . . . . 104

23 Multicellular Photosynthetic Autotrophs 107 23.1 Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 23.2 Plant phyla . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 23.3 Plant evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 23.4 Plant phylogeny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 23.5 Plant life cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 23.6 Moss life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 23.7 Vascular plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 23.8 Vascular plant life cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 23.9 Pterophyta (ferns) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 23.10 Non-seed plants, continued . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 23.11 Seed plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 23.12 Sporophyte/gametophyte . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 23.13 Megasporangium (nucellus) . . . . . . . . . . . . . . . . . . . . . . . . . . 110 23.14 Pollen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 23.15 Gymnosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 23.16 Pine life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 23.17 Other Coniferophyta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 23.18 Other gymnosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 23.19 Angiosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

VII

Contents

23.20 Earliest angiosperm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 23.21 Angiosperm flower . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 23.22 Angiosperm life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 23.23 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 23.24 Nutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 23.25 Fungal Reproduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 23.26 Types of Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 23.27 Key Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 23.28 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 23.29 Characteristics of an Animal . . . . . . . . . . . . . . . . . . . . . . . . . . 114 23.30 Introduction to animal phyla . . . . . . . . . . . . . . . . . . . . . . . . . 116 23.31 Phylum Porifera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 23.32 Phylum Cnidaria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 23.33 Phylum Platyhelminthes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 23.34 Phylum Rotifera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 23.35 Phylum Nematoda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 23.36 Phylum Annelida . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 23.37 Phylum Arthropoda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 23.38 Phylum Mollusca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 23.39 Phylum Echinodermata . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 23.40 Phylum Chordata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

24 Chordates 127 24.1 Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 24.2 Subphylum Urochordata . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 24.3 Subphylum Cephalochordata . . . . . . . . . . . . . . . . . . . . . . . . . 128 24.4 Subphylum Vertebrata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

25 Tissues and Systems 135

26 Epithelial tissue 137

27 Connective tissue 139

28 Muscle tissue 143

29 Vertebrate digestive system 147

30 Circulatory system 151

31 Respiratory system 155 31.1 Neuron structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156 31.2 Central nervous system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 31.3 Peripheral nervous system . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

32 Sensory systems 159 32.1 Taste and smell (chemoreception) . . . . . . . . . . . . . . . . . . . . . . . 159 32.2 Response to gravity and movement . . . . . . . . . . . . . . . . . . . . . . 159 32.3 Vision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160

VIII

Contents

32.4 Homeostasis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 32.5 Osmotic environments and regulations . . . . . . . . . . . . . . . . . . . . 161

33 Additional material 165 33.1 External Links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

34 Glossary 167 34.1 Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168

35 Contributors 169

List of Figures 175

36 Licenses 179 36.1 GNU GENERAL PUBLIC LICENSE . . . . . . . . . . . . . . . . . . . . 179 36.2 GNU Free Documentation License . . . . . . . . . . . . . . . . . . . . . . 180 36.3 GNU Lesser General Public License . . . . . . . . . . . . . . . . . . . . . . 181

1 Getting Started

2 Biology - The Life Science

The word biology means, "the science of life", from the Greek bios, life, and logos, word or knowledge. Therefore, Biology is the science of Living Things. That is why Biology is sometimes known as Life Science.

The science has been divided into many subdisciplines, such as botany1, bacteriology, anatomy2, zoology, histology, mycology, embryology, parasitology, genetics3, molecular biol- ogy4, systematics, immunology, microbiology5, physiology, cell biology6, cytology, ecology7, and virology. Other branches of science include or are comprised in part of biology studies, including paleontology8, taxonomy, evolution, phycology, helimentology, protozoology, en- tomology, biochemistry, biophysics, biomathematics, bio engineering, bio climatology and anthropology.

2.1 Characteristics of life

Not all scientists agree on the definition of just what makes up life. Various characteristics describe most living things. However, with most of the characteristics listed below we can think of one or more examples that would seem to break the rule, with something nonliving being classified as living or something living classified as nonliving. Therefore we are careful not to be too dogmatic in our attempt to explain which things are living or nonliving.

• Living things are composed of matter structured in an orderly way where simple molecules are ordered together into much larger macromolecules.

An easy way to remember this is GRIMNERD C All organisms; - Grow, Respire, Interact, Move, Need Nutrients, Excrete (Waste), Reproduce,Death, Cells (Made of)

• Living things are sensitive, meaning they are able to respond to stimuli.

• Living things are able to grow, develop, and reproduce.

• Living things are able to adapt over time by the process of natural selection.

• All known living things use the hereditary molecule, DNA9.

1 http://en.wikibooks.org/wiki/botany 2 http://en.wikibooks.org/wiki/anatomy 3 http://en.wikibooks.org/wiki/genetics 4 http://en.wikibooks.org/wiki/Molecular%20Biology 5 http://en.wikibooks.org/wiki/microbiology 6 http://en.wikibooks.org/wiki/Cell%20Biology 7 http://en.wikibooks.org/wiki/ecology 8 http://en.wikibooks.org/wiki/paleontology 9 http://en.wikipedia.org/wiki/DNA

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http://en.wikibooks.org/wiki/microbiology
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http://en.wikibooks.org/wiki/ecology
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http://en.wikipedia.org/wiki/DNA
Biology - The Life Science

• Internal functions are coordinated and regulated so that the internal environment of a living thing is relatively constant, referred to as homeostasis10.

Living things are organized in the microscopic level from atoms up to cells11. Atoms are arranged into molecules, then into macromolecules12, which make up organelles13, which work together to form cells. Beyond this, cells are organized in higher levels to form entire multicellular organisms. Cells together form tissues14, which make up organs, which are part of organ systems, which work together to form an entire organism. Of course, beyond this, organisms form populations which make up parts of an ecosystem. All of the Earth's ecosystems together form the diverse environment that is the earth.

Example:-

sub atoms, atoms, molecules, cells, tissues, organs, organ systems, organisms, population, community, eco systems

2.2 Nature of science

Science is a methodology for learning about the world. It involves the application of knowledge.

The scientific method deals with systematic investigation, reproducible results, the formation and testing of hypotheses, and reasoning.

Reasoning can be broken down into two categories, induction (specific data is used to develop a generalized observation or conclusion) and deduction (general information leads to specific conclusion). Most reasoning in science is done through induction.

Science as we now know it arose as a discipline in the 17th century.

2.3 Scientific method

The scientific method is not a step by step, linear process. It is an intuitive process, a methodology for learning about the world through the application of knowledge. Scientists must be able to have an "imaginative preconception" of what the truth is. Scientists will often observe and then hypothesize the reason why a phenomenon occurred. They use all of their knowledge and a bit of imagination, all in an attempt to uncover something that might be true. A typical scientific investigation might go like so:

You observe that a room appears dark, and you ponder why the room is dark. In an attempt to find explanations to this curiosity, your mind unravels several different hypotheses. One hypothesis might state that the lights are turned off. Another hunch might be that the room's lightbulb has burnt out. Worst yet, you could be going blind. To discover the truth,

10 http://en.wikipedia.org/wiki/homeostasis 11 http://en.wikipedia.org/wiki/cell 12 http://en.wikipedia.org/wiki/macromolecule 13 http://en.wikipedia.org/wiki/organelle 14 http://en.wikibooks.org/wiki/General%20Biology%2FTissues

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http://en.wikipedia.org/wiki/macromolecule
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Scientific method

you experiment. You feel your way around the room and find a light switch and turn it on. No light. You repeat the experiment, flicking the switch back and forth. Still nothing. That means your initial hypothesis, the room is dark because the lights are off, has been rejected. You devise more experiments to test your hypotheses, utilizing a flashlight to prove that you are indeed not blind. In order to accept your last remaining hypothesis as the truth, you could predict that changing the light bulb will fix the problem. If all your predictions succeed, the original hypothesis is valid and is accepted. In some cases, however, your predictions will not occur, in which you'll have to start over. Perhaps the power is off.

Figure 1 How Science is Done A diagram that illustrates scientific investigation

Scientists first make observations that raise a particular question. In order to explain the observed phenomenon, they develop a number of possible explanations, or hypotheses. This is the inductive part of science, observing and constructing plausible arguments for why

Biology - The Life Science

an event occurred. Experiments are then used to eliminate one of more of the possible hypotheses until one hypothesis remains. Using deduction, scientists use the principles of their hypothesis to make predictions, and then test to make sure that their predictions are confirmed. After many trials (repeatability) and all predictions have been confirmed, the hypothesis then may become a theory.

Quick Definitions

Observation - Quantitative and qualitative measurements of the world.

Inference - Deriving new knowledge based upon old knowledge.

Hypotheses - A suggested explanation.

Rejected Hypothesis - An explanation that has been ruled out through experimentation.

Accepted Hypothesis - An explanation that has not been ruled out through excessive experimentation and makes verifiable predictions that are true.

Experiment - A test that is used to rule out a hypothesis or validate something already known.

Scientific Method - The process of scientific investigation.

Theory - A widely accepted hypothesis that stands the test of time. Often tested, and usually never rejected.

The scientific method is based primarily on the testing of hypotheses by experimentation. This involves a control, or subject that does not undergo the process in question. A scientist will also seek to limit variables to one or another very small number, single or minimum number of variables. The procedure is to form a hypothesis or prediction about what you believe or expect to see and then do everything you can to violate that, or falsify the hypotheses. Although this may seem unintuitive, the process serves to establish more firmly what is and what is not true.

A founding principle in science is a lack of absolute truth: the accepted explanation is the most likely and is the basis for further hypotheses as well as for falsification. All knowledge has its relative uncertainty.

Theories are hypotheses which have withstood repeated attempts at falsification. Common theories include evolution by natural selection and the idea that all organisms consist of cells. The scientific community asserts that much more evidence supports these two ideas than contradicts them.

Charles Darwin

2.4 Charles Darwin

Figure 2

Charles Darwin is most remembered today for his contribution of the theory of evolution through natural selection.

The seeds of this theory were planted in Darwin's mind through observations made on a five-year voyage through the New World on a ship called the Beagle. There, he studied fossils and the geological record, geographic distribution of organisms, the uniqueness and relatedness of island life forms, and the affinity of island forms to mainland forms.

Upon his return to England, Darwin pondered over his observations and concluded that evolution must occur through natural selection. He declined, however, to publish his work because of its controversial nature. However, when another scientist, Wallace, reached similar conclusions, Darwin was convinced to publish his observations in 1859. His hypothesis revolutionized biology and has yet to be falsified by empirical data collected by mainstream scientists.

2.5 After Darwin

Since Darwin's day, scientists have amassed a more complete fossil record, including microorganisms and chemical fossils. These fossils have supported and added subtleties to Darwin's theories. However, the age of the Earth is now held to be much older than Darwin thought. Researchers have also uncovered some of the preliminary mysteries of the mechanism of heredity as carried out through genetics and DNA, areas unknown to Darwin. Another growing area is comparative anatomy including homology and analogy.

Today we can see a bit of evolutionary history in the development of embryos, as certain (although not all) aspects of development recapitulate evolutionary history.

Biology - The Life Science

The molecular biology15 study of slowly mutating genes reveal considerable evolutionary history consistent with fossil and anatomical record.

2.6 Challenges to Darwin

Figure 3

Darwin and his theories have been challenged many times in the last 150 years. The challenges have been primarily religious based on a perceived conflict with the preconceived notion of creationism. Many of those who challenge Darwin have been adherents to the young earth hypothesis that says that the Earth is only some 6000 years old and that all species were individually created by a god. Some of the proponents of these theories have suggested that chemical and physical laws that exist today were different or nonexistent in earlier ages. However, for the most part, these theories are either not scientifically testable and fall outside the area of attention of the field of biology, or have been disproved by one or more fields of science.

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of Cleveland State University.

15 http://en.wikibooks.org/wiki/molecular%20biology

http://en.wikibooks.org/wiki/molecular%20biology
3 The Nature of Molecules

3.1 Matter

Matter is defined as anything that has mass1 (an amount of matter in an object) and occupies space2 (which is measured as volume3).

• Particles, from smallest to largest 1. Subatomic particles

• Electrons4 • Protons5 • Neutrons6

2. Atoms 3. Molecules 4. Macromolecules

• Origin of matter 1. Big Bang7, about 13.7 billion years ago 2. Hydrogen8, helium9 3. Heavier elements formed in suns, super nova

• Earth's matter predates formation of sun, 4.5 billion years ago • All matter consists of atoms, which are composed of : electrons, protons, neutrons

3.2 The atom

• Example: Hydrogen • The simplest element • One proton (+) • One electron in orbit (-)

• Built by adding one proton (and one electron) at a time • Number of protons determines atomic number and number of electrons • Neutrons

• Neutral charge

1 http://en.wikipedia.org/wiki/mass 2 http://en.wikipedia.org/wiki/space%23Physics 3 http://en.wikipedia.org/wiki/volume 4 http://en.wikipedia.org/wiki/Electrons 5 http://en.wikipedia.org/wiki/Protons 6 http://en.wikipedia.org/wiki/Neutrons 7 http://en.wikipedia.org/wiki/Big%20Bang 8 http://en.wikipedia.org/wiki/Hydrogen 9 http://en.wikipedia.org/wiki/Helium

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The Nature of Molecules

• Contribute mass • May decay

• Oxygen10 • 8 protons (mass) • 8 electrons • 8 neutrons (mass)

3.3 Mass and isotopes

• Atomic mass • Sum of masses of protons and neutrons • Measured in daltons or AMU (Atomic Mass Unit) • An AMU is 1/12 the mass of Carbon-12 • proton ˜1 AMU or dalton • 6.024 x 1023 daltons/gram

• Atoms with same atomic number belong to same element • Isotopes

• Same atomic number but different atomic mass • Some are radioactive • Uses of isotopes

• Radioactive: 3H, 14C, 32P, 35S • Tracers in biochemical reactions • Detection of molecules in recombinant DNA technology (genetic engineering) • Half-life: dating of rocks, fossils

• Non-radioactive (N, C, O) • Diet of organisms (including fossils) • Biochemical tracers

3.4 Electrons

• Negative charge • Held in orbit about nucleus by attraction to positively charged nucleus • Atom may gain or lose electron, altering charge

• Cation: loses electron, positive charge • Na+

• Anion: gains electron, negative charge • Cl-

• Determine chemical properties of atoms • Number • Energy level

10 http://en.wikipedia.org/wiki/Oxygen

http://en.wikipedia.org/wiki/Oxygen
Chemical bonds

3.5 Chemical bonds

• Form molecules • Enzymes: make, break, rearrange chemical bonds in living systems • Ionic • Covalent

• Sharing of one or more pairs of electrons • Called single, double, or triple

• No net charge (as in ionic bonds) • No free electrons • Give rise to discrete molecules • Hydrogen

3.6 Chemical reactions

• Formation and breaking of chemical bonds • Shifting arrangement of atoms • Reactants -> products • Reactions are influenced by:

• Temperature • Concentration of reactants, products • Presence of catalysts (enzymes)

• Oxidation:reduction

3.7 Water

• Essential for life • ˜75% earth's surface is water • Life evolved in water • Solvent for many types of solutes • High specific heat • High polarity

• Creates a slightly negative Oxygen and a Slightly positive hydrogen • allows formation of Hydrogen Bonds

3.7.1 Hydrogen bonding

• A type of polar interaction • Critical for:

• Protein structure • Enzymatic reactions • Movement of water in plant stems

• Weak and transient • Powerful cumulative effect

The Nature of Molecules

• Solubility of many compounds • Cohesion (capillary action) • Lower density of ice

• Formed between molecules other than water • Protein structure • DNA11, RNA12 structure

Water organizes nonpolar molecules

• Nonpolar molecules: no polarity (+/-) charges • Hydrophobic: exclude water because they don't form hydrogen bonds with it • Consequences:

• Membranes • Protein structure

• Hydrophilic: polar substances associate with water

Ionization of water: H2O -> H+ + OH-

• Forms a Hydrogen ion (H+), hydroxide ion (OH-) • Due to spontaneous breakage of covalent bond • At 25°C, 1 liter of water contains 10-7 moles of H+ ions: 10-7 moles/liter

• A convenient way of indicating H+ concentration • pH13 = -log[H+] • For water, pH = -log[10-7] = 7 • Since for each H+ in pure water, there is one OH-, pH of 7 indicates neutrality • Logarithmic scale

Buffer

• Reservoir for H+ • Maintains relatively constant pH over buffering range

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.

11 http://en.wikipedia.org/wiki/DNA 12 http://en.wikipedia.org/wiki/RNA 13 http://en.wikipedia.org/wiki/pH

http://en.wikipedia.org/wiki/DNA
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4 The Chemical Building Blocks of Life

Building blocks of life

• Carbon based: organic molecules • Carbohydrates: CHO • Lipids: CHO, water insoluble • Proteins: CHONS, structure/function in cells • Nucleic acids: CHONP, hereditary (genetic) information

4.1 Carbon

• Can make 4 covalent bonds1 • Chains

• Straight • Branched • Ring

• Hydrocarbons2 (C, H): store energy • Functional groups

• Attach to carbon • Alter chemical properties • Form macromolecules • Sapoteton

4.2 Carbohydrates

• Principally CHO (rare N, S and P) • 1C:2H:1O ratio • Energy rich (many C-H bonds)

• Monosaccharides (principal: glucose3) • Simple sugars • Principle formula: C6H12O6 • Form rings in water solution

• Disaccharides (sucrose, lactose) • Polysaccharides (starch, glycogen, cellulose, chitin)

1 http://en.wikipedia.org/wiki/covalent%20bonds 2 http://en.wikipedia.org/wiki/Hydrocarbons 3 http://en.wikipedia.org/wiki/glucose

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The Chemical Building Blocks of Life

4.3 Stereoisomers

• Bond angles of carbon point to corners of a tetrahedron • When 4 different groups are attached to a carbon, it is asymmetric, leading to various

types of isomerism • Stereoisomers: (D, L)

• Same chemical properties • Different biological properties • D sugars, L amino acids

4.4 Lipids

• C-H bonds (nonpolar) instead of C-OH bonds as in carbohydrates • High energy • Hydrophobic (insoluble in water)

• Categories • Fats: glycerol and three fatty acids • Phospholipids: primary component of membranes • Prostaglandins: chemical messengers (hormones) • Steroids: membrane component; hormones • Terpenes: pigments; structure

4.4.1 Fatty acids

• Hydrocarbon chain • Even number of C, 14->20 • Terminates in carboxyl group

• Saturated: contain maximum number of hydrogens (all single bonds); maximum energy • Unsaturated: one or more double bonds

• Usually higher melting point • Many common oils are polyunsaturated

4.5 Proteins

• Polymer of amino acids • 21 different amino acids found in proteins • Sequence of amino acids determined by gene

• Amino acid sequence determines shape of molecule • Linked by peptide bond (covalent)

• Functions • regulate chemical reactions and cell processes [enzymes] • form bone and muscle; various other tissues • facilitate transport across cell membrane [carrier proteins]

Proteins

• fight disease [antibodies] • Motifs: folding patterns of secondary structure • Domains: structural, functional part of protein often independent of another part; often

encoded by different exons • Shape determines protein's function

4.5.1 Amino acids

• 21 commonly found in proteins • 21st is selenocysteine, not mentioned in text

• Common structure • Amino group: NH2 • Carboxyl group: COOH • R group- 4 different kinds of R groups

• acidic • basic • hydrophilic (polar) • hydrophobic (nonpolar)

• Confer individual properties on amino acids • List of amino acids4

4.5.2 Structure

• Primary structure: the amino acid sequence • Determines higher orders of structure • Critical for structure and function of protein

• Secondary: stabilized by intramolecular hydrogen bonding • helix • sheet

• Tertiary: folding, stabilized by ionic bonds (between R groups), hydrogen bonding, van der Waal's forces, hydrophobic interactions

• Quaternary: _2 polypeptides

4.5.3 Function

• Requires proper folding, cofactors, pH, temperature, etc. • Proteins are often modified after synthesis

• Chemical modification • Addition of heme groups (hemoglobin, cytochrome)

• Denatured proteins can not function properly • Proteins are degraded by proteosome as part of constant turnover of cell components

4 http://en.wikipedia.org/wiki/Amino%20acid%23List%20of%20amino%20acids

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The Chemical Building Blocks of Life

4.6 Hereditary (Genetic) information

• Nucleic acids • DNA: deoxyribonucleic acid

• Hereditary information of all cells • Hereditary information for many viruses

• RNA: ribonucleic acid • Hereditary information of certain viruses (HIV5) • Intermediate in gene expression • Composed of nucleotides

• Ribonucleotides • Deoxyribonucleotides

4.6.1 RNA DNA origin

• Which came first? • Paradox: DNA encodes protein necessary for its own replication • Discovery of catalytic RNA by Cech and Altman suggested that RNA might have been

first self-replicating molecule • DNA evolved as more stable type of storage molecule

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.

Proteins: Their building block is amino acids. The bond connecting 2 of the amino acids together are called peptide bonds. One of these bonds makes a monopeptide, two a dipeptide, and any more than that makes a polypeptide.

5 http://en.wikipedia.org/wiki/HIV

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5 Life: History and Origin

5.1 Properties of life

1. Organization: Being structurally composed of one or more cells, which are the basic units of life. • prokaryote: no nucleus • eukaryote: membrane bound nucleus.

2. Sensitivity: respond to stimuli.

3. Energy Processing

4. Growth and Development

5. Reproduction

• hereditary mechanisms to make more of self; DNA based. 6. Regulation, including homeostasis.

7. Evolution.

5.2 Origin of life: 3 hypotheses

• Extraterrestrial origin (panspermia): meteor, comet borne from elsewhere in universe • evidence of amino acids and other organic material in space (but often both D & L

forms) • questionable bacterial fossils in Martian rock

-However, this would imply that some other origin of life was likely because it would have had to happen elsewhere before it could be transported here, and the only difference would be that life did not originate on Earth.

• Spontaneous origin on earth: primitive self-replicating macromolecules acted upon by natural selection ((macro)Evolution is one example of this)

-This is often attacked for the seeming impossibility for life to have been produced by a chemical reaction triggered by lightning and the ability of any produced DNA to actually be in a sequence that could produce a working model of life if replicated. It is also attacked for religious reasons, as it bypasses things like the idea of a supreme being directly creating humans. It also seems unlikely to some that such huge changes are possible in evolution

Life: History and Origin

without evidence of an "in-between stage" that is credible. Many of the stages of man are disputed due to their somewhat shakey grounds. For example, bones from other animals have been taken accidentally in some cases to be part of a humanoid, and complete skeletons have been sketched out from a limited number of bones.

• Special creation: religious explanations (Intelligent Design is one popular example of this.) These explanations contend that life was created by God (or perhaps some other Intelligent Designer). • Proponents of Intelligent design suggest that the vast complexity of life could only

have been intentionally designed while other creationists cite biblical support.

-This is often attacked for many of the same reasons that religion is attacked, and is often regarded as superstitious and/or unscientific.

• It is debated as to whether schools should teach one hypothesis or the other when talking about the origin of life. However, since they are all currently known major hypotheses (and sometimes hypotheses proven wrong are shown for educational purposes), this wikibook includes what it can without discriminating unfairly against one hypothesis or the other.

5.3 The early earth

It is believed that the Earth was formed about 4.5 billion years ago.

• Heavy bombardment by rubble ceased about 3.8 billion years ago. • Reducing atmosphere: much free H

• also H2O, NH3, CH4 • little, if any, free O2 • with numerous H electrons, require little energy to form organic compounds with C

• Warm oceans, estimated at 49-88°C • Lack of O2 and consequent ozone (O3) meant considerable UV energy

Chemical reactions on early earth

• UV and other energy sources would promote chemical reactions and formation of organic molecules

• Testable hypothesis: Miller-Urey experiment • simulated early atmospheric conditions • found amino acids, sugars, etc., building blocks of life • won Nobel prize for work • experiment showed prebiotic synthesis of biological molecules was possible

Issues

• Miller later conceded that the conditions in his experiments were not representative of what is currently thought to be those of early earth

• He also conceded that science has no answer for how amino acids could self-organize into replicating molecules and cells

• In the 50 years since Miller-Urey, significant issues and problems for biogenesis have been identified. This is a weak hypothesis at this time.

Origin of cells

• Conclusion: Life exists, we don't know why.

5.4 Origin of cells

Cells are very small and decompose quickly after death. As such, fossils of the earliest cells do not exist. Scientists have had to form a variety of theories on how cells (and hence life) was created on Earth.

• Bubble hypothesis • A. Oparin, J.B.S. Haldane, 1930’s

• Primary abiogenesis: life as consequence of geochemical processes • Protobionts: isolated collections of organic material enclosed in hydrophobic bubbles

• Numerous variants: microspheres, protocells, protobionts, micelles, liposomes, coacer- vates

• Other surfaces for evolution of life • deep sea thermal vents • ice crystals • clay surfaces • tidal pools

5.5 The RNA world?

• DNA → RNA → polypeptide (protein) • Catalytic RNA: ribozyme

• discovered independently by Tom Cech and Sid Altman (Nobel prize) • catalytic properties: hydrolysis, polymerization, peptide bond formation, etc.

• Self-replicating RNA molecule may have given rise to life • consistent with numerous roles for RNA in cells as well as roles for ribonucleotides

(ATP) • relationship to bubble-like structures is uncertain

5.6 The earliest cells

• Microfossils • ˜3.5 by • resemble bacteria: prokaryotes • biochemical residues • stromatolites

• Archaebacteria (more properly Archaea) • extremophiles: salt, acid, alkali, heat, methanogens • may not represent most ancient life

• Eubacteria • cyanobacteria: photosynthesis

• atmospheric O2; limestone deposits

Life: History and Origin

• chloroplasts of eukaryotes

Cyanobacteria

5.7 Major steps in evolution of life

• Prebiotic synthesis of macromolecules • Self replication

• RNA? (primitive metabolism) • DNA as hereditary material • 1st cells • Photosynthesis • Aerobic respiration • Multicellularity (more than once)

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.

6 Cells

7 Cell structure

7.1 What is a cell?

The word cell comes from the Latin word "cella", meaning "small room", and it was first coined by a microscopist observing the structure of cork. The cell is the basic unit of all living things, and all organisms are composed of one or more cells. Cells are so basic and critical to the study of life, in fact, that they are often referred to as "the building blocks of life". Organisms - bacteria, amoebae and yeasts, for example - may consist of as few as one cell, while a typical human body contains about a trillion cells.

According to Cell Theory, first proposed by Schleiden and Schwann in 1839, all life consists of cells. The theory also states that all cells come from previously living cells, all vital functions (chemical reactions) of organisms are carried out inside of cells, and that cells contain necessary hereditary information to carry out necessary functions and replicate themselves.

All cells contain:

• Lipid bilayer boundary (plasma membrane1) • Cytoplasm2 • DNA3 (hereditary information) • Ribosomes4 for protein synthesis

Eukaryotic cells also contain:

• At least one nucleus5 • Mitochondria6 for cell respiration and energy

Cells may also contain:

• Lysosomes7 • Peroxisomes8 • Vacuoles9 • Cell walls10

1 http://en.wikipedia.org/wiki/plasma%20membrane 2 http://en.wikipedia.org/wiki/Cytoplasm 3 http://en.wikipedia.org/wiki/DNA 4 http://en.wikipedia.org/wiki/Ribosome 5 http://en.wikipedia.org/wiki/Cell%20Nucleus 6 http://en.wikipedia.org/wiki/Mitochondrion 7 http://en.wikipedia.org/wiki/Lysosome 8 http://en.wikipedia.org/wiki/Peroxisome 9 http://en.wikipedia.org/wiki/Vacuole 10 http://en.wikipedia.org/wiki/Cell%20Wall

http://en.wikipedia.org/wiki/plasma%20membrane
http://en.wikipedia.org/wiki/Cytoplasm
http://en.wikipedia.org/wiki/DNA
http://en.wikipedia.org/wiki/Ribosome
http://en.wikipedia.org/wiki/Cell%20Nucleus
http://en.wikipedia.org/wiki/Mitochondrion
http://en.wikipedia.org/wiki/Lysosome
http://en.wikipedia.org/wiki/Peroxisome
http://en.wikipedia.org/wiki/Vacuole
http://en.wikipedia.org/wiki/Cell%20Wall
Cell structure

7.1.1 Concepts

Plasma Membrane

Phospholipid bilayer, which contains great amount of proteins, the most important functions are the following:

1. It selectively isolates the content of the cell of the external atmosphere. 2. It regulates the interchange of substances between the cytoplasm and the environment. 3. Communicates with other cells.

Model of the fluid mosaic

Describes the structure of the plasma membrane, this model was developed in 1972 by cellular biologists J. Singer and L. Nicholson.

Phospholipid bilayer

Is in the plasma membrane and produces the fluid part of membranes.

Proteins

Long chains of amino acids.

Glucose proteins

Proteins together with carbohydrates in the plasma membrane, mostly in the outer parts of the cell.

Functions of proteins

Transport oxygen, they are components of hair and nails, and allow the cell interact with its environment.

Transport Proteins

Regulate the movement of soluble water molecules, through the plasma membrane. Some transport proteins called channel proteins form pores or channels in the membrane so that water soluble molecules pass.

Carrying proteins

Have union sites that can hold specific molecules.

Reception proteins

They activate cellular responses when specific molecules join.

Proteins of recognition

They work as identifiers and as place of union to the cellular surface.

Fluid

It is any substance that can move or change of form.

Concentration

Number of molecules in a determined unit of volume.

What is a cell?

Gradient

Physical difference between two regions of space, in such a way that the molecules tend to move in response to the gradients.

Diffusion

Movement of the molecules in a fluid, from the regions of high concentration to those of low concentration.

Passive transport

Movement of substances in a membrane that doesn’t need to use energy.

Simple diffusion

Diffusion of water, gases or molecules across the membrane.

Facilitated diffusion

Diffusion of molecules across the membranes with the participation of proteins.

Osmosis

Diffusion of the water across a membrane with differential permeability.

Transport that needs energy

Movement of substances across a membrane generally in opposition to a gradient of concentration with the requirement of energy.

Active transport

Movement of small molecules using energy (ATP).

Endocytosis

Movement of big particles towards the interior of the cell using energy. The cells enclose particles or liquids.

Pinocytosis

(Literally cell drinking) Form in which the cell introduces liquids.

Phagocytosis

Way of eating of the cells. It feeds in this case of big particles or entire microorganisms.

Pseudopods

False feet (the amoeba).

Exocitosis

Movement of materials out of the cell with the use of energy. It throws waste material.

Isotonic

The cytoplasm fluid of the interior of the cells is the same that the outer.

Hypertonic solution

Cell structure

The solutions that have a higher concentration of dissolved particles than the cellular cytoplasm and that therefore water of the cells goes out with osmosis.

Hypotonic

The solutions with a concentration of dissolved particles lower than the cytoplasm of a cell and that therefore do that water enters the cell with osmosis.

Swelling

Pressure of the water inside the vacuole.

Endoplasmic Reticulum

It is the place of the synthesis of the cellular membrane.

7.1.2 Structure and function of the cell

Rudolf Virchow

Zoologist, who proposed the postulates of the cellular theory, observes that the living cells could grow and be in two places at the same time, he proposed that all the cells come from other equal cells and proposed 3 postulates:

1. Every living organism is formed from one or more cells 2. The smallest organisms are unicellular and these in turn are the functional units of

the multicellular organisms. 3. All the cells come from preexisting cells.

7.1.3 Common characteristics of all the cells

Molecular components

Proteins, amino acids, lipids, sweeten, DNA, RNA.

Structural components

Plasmatic membrane, citoplasm, ribosomes.

Robert Hooke

He postuled for the first time the term cell

Prokaryotes

Their genetic material is not enclosed in a membrane ex. Bacterias

Eukaryotes

Their genetic material is contained inside a nucleus closed by a membrane

History of cell knowledge

7.2 History of cell knowledge

The optical microscope was first invented in 17th century. Shortly thereafter scientists began to examine living and dead biological tissues in order to better understand the science of life. Some of the most relevant discovery milestones of the time period include:

• The invention of the microscope11, which allowed scientists for the first time to see biological cells

• Robert Hooke12 in 1665 looked at cork under a microscope and described what he called cork "cells"

• Anton van Leeuwenhoek13 called the single-celled organisms that he saw under the microscope "animalcules"

• Matthias Jakob Schleiden14, a botanist, in 1838 determined that all plants consist of cells

• Theodor Schwann15, a zoologist, in 1839 determined that all animals consist of cells • Rudolf Virchow16 proposed the theory that all cells arise from previously existing cells

In 1838, the botanist Matthias Jakob Schleiden and the physiologist Theodor Schwann discovered that both plant cells and animal cells had nuclei. Based on their observations, the two scientists conceived of the hypothesis that all living things were composed of cells. In 1839, Schwann published 'Microscopic Investigations on the Accordance in the Structure and Growth of Plants and Animals', which contained the first statement of their joint cell theory.

7.2.1 Cell Theory

Schleiden and Schwann proposed spontaneous generation as the method for cell origination, but spontaneous generation (also called abiogenesis17) was later disproven. Rudolf Virchow famously stated "Omnis cellula e cellula"... "All cells only arise from pre-existing cells." The parts of the theory that did not have to do with the origin of cells, however, held up to scientific scrutiny and are widely agreed upon by the scientific community today.

The generally accepted portions of the modern Cell Theory are as follows: (1) The cell is the fundamental unit of structure and function in living things. (2) All organisms are made up of one or more cells. (3) Cells arise from other cells through cellular division. (4) Cells carry genetic material passed to daughter cells during cellular division. (5) All cells are essentially the same in chemical composition. (6) Energy flow (metabolism and biochemistry) occurs within cells.

11 http://en.wikipedia.org/wiki/microscope 12 http://en.wikipedia.org/wiki/Robert%20Hooke 13 http://en.wikipedia.org/wiki/Anton%20van%20Leeuwenhoek 14 http://en.wikipedia.org/wiki/Matthias%20Jakob%20Schleiden 15 http://en.wikipedia.org/wiki/Theodor%20Schwann 16 http://en.wikipedia.org/wiki/Rudolf%20Virchow 17 http://en.wikipedia.org/wiki/Abiogenesis

http://en.wikipedia.org/wiki/microscope
http://en.wikipedia.org/wiki/Robert%20Hooke
http://en.wikipedia.org/wiki/Anton%20van%20Leeuwenhoek
http://en.wikipedia.org/wiki/Matthias%20Jakob%20Schleiden
http://en.wikipedia.org/wiki/Theodor%20Schwann
http://en.wikipedia.org/wiki/Rudolf%20Virchow
http://en.wikipedia.org/wiki/Abiogenesis
Cell structure

7.3 Microscopes

• Allow greater resolution, can see finer detail • Eye: resolution of ˜ 100 μm • Light microscope18: resolution of ˜ 200 nm • Limited to cells are larger organelles within cells • Confocal microscopy19: 2 dimension view • Electron microscope20: resolution of ˜0.2 nm • Laser tweezers: move cell contents

7.4 Cell size

One may wonder why all cells are so small. If being able to store nutrients is beneficial to the cell, how come there are no animals existing in nature with huge cells? Physical limitations prevent this from occurring. A cell must be able to diffuse gases and nutrients in and out of the cell. A cell's surface area does not increase as quickly as its volume, and as a result a large cell may require more input of a substance or output of a substance than it is reasonably able to perform. Worse, the distance between two points within the cell can be large enough that regions of the cell would have trouble communicating, and it takes a relatively long time for substances to travel across the cell.

That is not to say large cells don't exist. They are, once again, less efficient at exchanging materials within themselves and with their environment, but they are still functional. These cells typically have more than one copy of their genetic information, so they can manufacture proteins locally within different parts of the cell.

Key concepts: Cell size:

• Is limited by need for regions of cell to communicate • Diffuse oxygen and other gases • Transport of mRNA21 and protein22s

• Surface area to volume ratio limited • Larger cells typically:

• Have extra copies of genetic information • Have slower communication between parts of cell

18 http://en.wikipedia.org/wiki/Light%20microscope 19 http://en.wikipedia.org/wiki/microscopy 20 http://en.wikipedia.org/wiki/Electron%20microscope 21 http://en.wikipedia.org/wiki/RNA 22 http://en.wikipedia.org/wiki/protein

http://en.wikipedia.org/wiki/Light%20microscope
http://en.wikipedia.org/wiki/microscopy
http://en.wikipedia.org/wiki/Electron%20microscope
http://en.wikipedia.org/wiki/RNA
http://en.wikipedia.org/wiki/protein
8 Structure of Eukaryotic cells

Eukaryotic1 cells feature membrane delimited nucleii containing two or more linear chromo- some2s; numerous membrane-bound cytoplasmic organelles: mitochondria, RER3, SER4, lysosomes, vacuole5s, chloroplast6s; ribosomes and a cytoskeleton7. Also, plants, fungi, and some protists have a cell wall.

8.1 Structure of the nucleus

The nucleus is the round object in the cell that holds the genetic information (DNA) of the cell. It is surrounded by a nuclear envelope and has a nucleolus inside.

8.1.1 Nuclear envelope

The nuclear envelope is a double-layered plasma membrane8 like the cell membrane, although without membrane proteins. To allow some chemicals to enter the nucleus, the nuclear envelope has structures called Nuclear pore9s. The nuclear envelope is continuous with the endoplasmic reticulum.

8.1.2 Nucleolus

The nucleolus appears in a microscope as a small dark area within the nucleus. The nucleolus is the area where there is a high amount of DNA transcription10 taking place.

1 http://en.wikipedia.org/wiki/Eukaryote 2 http://en.wikipedia.org/wiki/chromosome 3 http://en.wikipedia.org/wiki/RER 4 http://en.wikipedia.org/wiki/SER 5 http://en.wikipedia.org/wiki/vacuole 6 http://en.wikipedia.org/wiki/chloroplast 7 http://en.wikipedia.org/wiki/cytoskeleton 8 http://en.wikibooks.org/wiki/Plasma%20membrane 9 http://en.wikibooks.org/wiki/Nuclear%20pore 10 http://en.wikibooks.org/wiki/DNA%20transcription

http://en.wikipedia.org/wiki/Eukaryote
http://en.wikipedia.org/wiki/chromosome
http://en.wikipedia.org/wiki/RER
http://en.wikipedia.org/wiki/SER
http://en.wikipedia.org/wiki/vacuole
http://en.wikipedia.org/wiki/chloroplast
http://en.wikipedia.org/wiki/cytoskeleton
http://en.wikibooks.org/wiki/Plasma%20membrane
http://en.wikibooks.org/wiki/Nuclear%20pore
http://en.wikibooks.org/wiki/DNA%20transcription
Structure of Eukaryotic cells

8.2 Chromatin

Chromosomes consist of chromatin11. This is made up of strings of DNA, which typically measure centimeters in length if stretched out. This DNA is wound around a histone12 core and organized into nucleosome13s.

The chromatin14 must be uncoiled for gene expression15 and replication16. Chromosome micrograph

8.3 Endoplasmic reticulum

The endoplasmic reticulum17 is a cellular organelle18 made up of a series of extended folded intracellular membranes. It is continuous with the nuclear membane.

There are two main types of endoplasmic reticulum:

• RER: rough endoplasmic reticulum (site of protein synthesis19) associated with ribosomes • SER: smooth endoplasmic reticulum (site of lipid synthesis20)

8.3.1 Rough Endoplasmic Reticulum

Proteins are directed to the RER by a signal sequence of a growing polypeptide21s on the ribosome. This is recognised by a signal recognition particle which brings the ribo- some/polypeptide complex to a channel on the RER called a translocon. At the translocon, the signal sequence and ribosome/polypeptide complex interact with the translocon to open it. The signal sequence becomes attached to the translocon. The ribosome can continue to translate the polypeptide into the lumen of the RER. As synthesis continues, 2 processes can happen.

1. If the protein is destined to become a membrane bound protein then the protein synthesis will continue until termination. The ribosome can then dissociate, allowing protein folding within the RER lumen to occur and continuation to the golgi apparatus for processing of the polypeptide.

2. If the protein is destined for storage for later secretion after stimulation or for continuous secretion then a protease-enzyme which cuts proteins at the peptide bond-can cut the signal sequence from the growing polypeptide. Continuation to the golgi etc. can then occur.

11 http://en.wikipedia.org/wiki/chromatin 12 http://en.wikipedia.org/wiki/histone 13 http://en.wikipedia.org/wiki/nucleosome 14 http://en.wikipedia.org/wiki/chromatin 15 http://en.wikipedia.org/wiki/gene%20expression 16 http://en.wikipedia.org/wiki/replication 17 http://en.wikipedia.org/wiki/endoplasmic%20reticulum 18 http://en.wikipedia.org/wiki/organelle 19 http://en.wikipedia.org/wiki/protein%20synthesis 20 http://en.wikipedia.org/wiki/lipid%20synthesis 21 http://en.wikipedia.org/wiki/polypeptide

http://en.wikipedia.org/wiki/chromatin
http://en.wikipedia.org/wiki/histone
http://en.wikipedia.org/wiki/nucleosome
http://en.wikipedia.org/wiki/chromatin
http://en.wikipedia.org/wiki/gene%20expression
http://en.wikipedia.org/wiki/replication
http://en.wikipedia.org/wiki/endoplasmic%20reticulum
http://en.wikipedia.org/wiki/organelle
http://en.wikipedia.org/wiki/protein%20synthesis
http://en.wikipedia.org/wiki/lipid%20synthesis
http://en.wikipedia.org/wiki/polypeptide
Endoplasmic reticulum

When produced, proteins are then exported to one of several locations. The proteins are either modified for extracellular membrane insertion or secretion. Note, this is in contrast with ribosomes which do not associate with the RER and produce proteins which will become cytosolic enzymes for example.

8.3.2 Smooth Endoplasmic Reticulum

Smooth endoplasmic reticulum produces enzyme22s for lipid and carbohydrate biosynthesis and detoxification RER

8.3.3 Sarcoplasmic Reticulum

This is a specialised form of endoplasmic reticulum found in some muscle cell types- particularly striated, skeletal muscle. Its main function is different from the other 2 types in that is mainly acts as a storage of calcium. This reticulum has voltage gated channels which respond to signals from 'motor neurones' to open and release calcium into the cytoplasm. This can then bring about the next part in muscle contraction.

Figure 4

Figure 1 :Image of nucleus23, endoplas- mic reticulum and Golgi apparatus.

1. Nucleus. 2. Nuclear pore. 3. Rough endoplasmic reticulum (RER). 4. Smooth endoplasmic reticulum (SER). 5. Ribosome on the rough ER. 6. Proteins that are transported. 7. Transport vesicle. 8. Golgi apparatus. 9. Cis face of the Golgi apparatus. 10. Trans face of the Golgi apparatus. 11. Cisternae of the Golgi apparatus. 1.

22 http://en.wikipedia.org/wiki/enzyme 23 http://en.wikipedia.org/wiki/cell%20nucleus

http://en.wikipedia.org/wiki/enzyme
http://en.wikipedia.org/wiki/cell%20nucleus
Structure of Eukaryotic cells

8.4 The Golgi apparatus

The golgi apparatus24 is made up of multiple stacks of bilipid membranes.

• Proteins made on the RER are modified and then sorted • Formation of secretory vesicles • Formation of lysosomes (intracellular digestion)

Other membrane-bound cytoplasmic organelles include:

• Microbodies25 (generic term) • Glyoxysome (transforms fat into carbohydrate in plants) • Peroxisome26 (uses oxidative metabolism to form hydrogen peroxide and is destroyed by

catalase27)

8.5 Ribosomes

Ribosomes are the site of protein synthesis. Ribosomes themselves are synthesized in the cell nucleoli28 and are structured as two subunits, the large and the small. These parts are composed of RNA and protein.

Prokaryotic and eukaryotic ribosomes are different, the eukaryotic ones being larger and more complicated.

8.6 DNA-containing organelles

Mitochondria

• Double membrane • Aerobic metabolism, internal membrane • DNA, ribosomes • Give rise to new mitochondria

Chloroplast29

• Double membrane • Photosynthesis, internal membrane • DNA, ribosomes • Give rise to new chloroplasts

Centriole30s

24 http://en.wikipedia.org/wiki/Golgi%20apparatus 25 http://en.wikipedia.org/wiki/Microbody 26 http://en.wikipedia.org/wiki/Peroxisome 27 http://en.wikipedia.org/wiki/catalase 28 http://en.wikipedia.org/wiki/nucleoli 29 http://en.wikipedia.org/wiki/Chloroplast 30 http://en.wikipedia.org/wiki/Centriole

http://en.wikipedia.org/wiki/Golgi%20apparatus
http://en.wikipedia.org/wiki/Microbody
http://en.wikipedia.org/wiki/Peroxisome
http://en.wikipedia.org/wiki/catalase
http://en.wikipedia.org/wiki/nucleoli
http://en.wikipedia.org/wiki/Chloroplast
http://en.wikipedia.org/wiki/Centriole
Cytoskeleton

• Microtubule organizing centers • Animal cells and many protists • Pair constitutes the centrosome • Give rise to flagellum during spermatogenesis

• Consist of 9 triplet microtubules • Mitosis31, meiosis32

8.7 Cytoskeleton

Cytoskeleton is a collective term for different filaments of proteins that can give physical shape within the cell and are responsible for the 'roads' which organelles can be carried along.

• Gives the cell shape • Anchors other organelles • Vital to intracellular transport of large molecules

The cytoskeleton is composed of 3 main types of filaments:

• Actin33 filaments (7 nm) • Microtubule34s: (25 nm) polymer of tubulin; 13/ring. • Intermediate Filament35s

Both actin and microtubules can have associated motor proteins.

8.7.1 Intermediate Filaments

These are rope like filaments, 8-10nm in diameter and tend to give the structural stability to cells. Examples inculude Vimentin, neurofilaments and keratin. It is keratin which priniciply makes up hair, nails and horns.

8.7.2 Actin Filaments

Growth These filaments are 2-stranded and composed of dimeric subunits called G-Actin. They contain a GTP molecule in order to bind (polymerise). As GTP is hydrolysed then the structure becomes unstable and depolymerisation occurs. The growth of actin filaments is concentration dependant-that is, the higher the concentration of free G-actin, the greater the polymerisation. The are also polar, having a + and a - end (not related to charge) and polymerisation tends to happen faster at the + end.

31 http://en.wikipedia.org/wiki/mitosis 32 http://en.wikipedia.org/wiki/meiosis 33 http://en.wikipedia.org/wiki/Actin 34 http://en.wikipedia.org/wiki/Microtubule 35 http://en.wikipedia.org/wiki/Intermediate%20Filament

http://en.wikipedia.org/wiki/mitosis
http://en.wikipedia.org/wiki/meiosis
http://en.wikipedia.org/wiki/Actin
http://en.wikipedia.org/wiki/Microtubule
http://en.wikipedia.org/wiki/Intermediate%20Filament
Structure of Eukaryotic cells

Cilia and flagella are threads of microtubules that extend from the exterior of cells and used to move single celled organisms as well as move substances away from the surface of the cell. motor proteins-move, wave motion

9 Membranes

9.1 Biological membranes

Figure 5 Plasma membrane bilayer

Membranes

Biological membranes surround cells and serve to keep the insides separated from the outsides. They are formed of phospholipid bilayer1s, which by definition are a double layer of fatty acid2 molecules (mostly phospholipid3s, lipids containing lots of phosphorus).

Proteins4 serve very important functions in cellular membranes. They are active transports in and out of the cell, acting as gatekeepers. They relay signals in and out of the cell. Proteins are the site of many enzymatic reactions in the cell, and play a role in regulation of cellular processes.

9.2 Phospholipid

Phospholipid bilayer

• basis of biological membranes and cellular organisms • contains a charged, hydrophilic (attracted to water) head and two hydrophobic (repelled

by water) hydrocarbon tails • In presence of water, phospholipids form bilayer

• maximize hydrogen bonds between water • creates barrier to passage of materials • fluid mosaic model shows horizontal (common) and "flip-flop" (rare) movement of

phospholipids

9.3 Fluid mosaic model

• Current model of membrane • Phospholipid bilayer

• Phospholipids • Move freely in lipid layer, but rarely switch layers • Different phospholipids in each layer in different organelles

• Glycolipids • Sterols (cholesterol in animals)

• Transmembrane proteins "float" in fluid lipid bilayer • also called intrinsic, integral proteins

• Exterior (extrinsic, peripheral) proteins

9.4 Membrane proteins

• Transport channels • Enzymes • Cell surface receptors

1 http://en.wikibooks.org/wiki/lipid%20bilayer 2 http://en.wikibooks.org/wiki/Fatty%20acid 3 http://en.wikibooks.org/wiki/phospholipid 4 http://en.wikibooks.org/wiki/Proteins

http://en.wikibooks.org/wiki/lipid%20bilayer
http://en.wikibooks.org/wiki/Fatty%20acid
http://en.wikibooks.org/wiki/phospholipid
http://en.wikibooks.org/wiki/Proteins
Membrane proteins

• Cell surface identity markers • Cell adhesion proteins • Attachments to cytoskeleton

Integral membrane proteins

• Anchoring to membrane • Protein has attached phosphatidylinositol (GPI) linkage, anchors protein in outer

layer (no picture) • Protein has one or more hydrophobic transmembrane domains

• -helix • -sheet

Channel protein Transport across membranes * Diffusion

• • From higher concentration to lower concentration • Membranes are selectively permeable

• Ions diffuse through membrane channels • Selective • Movement determined by diffusion and voltage differences

• Facilitated diffusion • Carrier protein, physically binds transported molecule

• Osmosis • Diffusion of water down concentration gradient • In cell: various solutes (amino acids, ions, sugars, etc.)

• interact with water, e.g., hydration shells • Water moves through aquaporin channels into cell • Depends upon the concentration of all solutes in solution

• Hyperosmotic solution: higher concentration of solutes • Hypoosmotic solution: lower concentration of solutes • Isoosmotic solution: solute concentrations equal

• Water moves from hypoosmotic solution to hyperosmotic solution

Osmotic pressure Bulk transport

• Endocytosis: energy requiring • Phagocytosis

• Solid material, typically food • Pinocytosis

• Primarily liquid

** Receptor-mediated endocytosis

• Pits on cell surface coated with clathrin and receptors • Bind specific proteins • Exocytosis

• Discharge of materials from vesicle at cell surface

Membranes

9.5 Receptor-mediated endocytosis

Active transport

• Energy required (usually ATP) • Highly selective • Works against concentration gradient • Many examples, e.g., Na+/K+ pump

Cotransport (coupled transport)

• Does not use ATP directly • Molecule is transported in connection with another molecule that is moving down a

concentration gradient • Example: Na+ gradient is established by a Na+ pump, with higher concentration on

outside of cell. Cotransport channel carries Na+ and another molecule (e.g. glucose) into cell

• May involve proton (H+) pumps (chemiosmosis - ATP production)

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.

10 Cell-cell interactions

with the environment with each other

10.1 Cell signaling

• Signaling requires • Signal • Cell receptor (usually on surface)

• Signaling is important in: • Response to environmental stimuli • Sex • Development

• Major area of research in biology today

10.1.1 Types of signaling

• Direct contact (e.g., gap junctions between cells) • Paracrine: Diffusion of signal molecules in extracellular fluid; highly local • Endocrine: Signal (hormone) molecule travels through circulatory system • Synaptic: neurotransmitters

Types of signal molecules

• Hormones: chemically diverse • Steroid • Polypeptide • Vitamin/amino acid derived

• Cell surface proteins/glycoproteins • Ca2+, NO • Neurotransmitter

• Several hundred types • Some are also hormones e.g. Estrogen, progesterone

Receptor molecules

• Intracellular • Protein that binds signal molecule in cytoplasm

Cell-cell interactions

• Bound receptor may act as: • Gene regulator • Enzyme • Cell surface

• Gated ion channels (neurotransmitter receptor) • Enzymic receptors • G protein-linked receptors

Cell surface protein

• Tissue identity • glycolipids • MHC proteins

• Immune systems • distinguish self from not-self

• Intercellular adhesion • permanent contact • help form sheets of cells, tissues • may permit signaling

Example: G proteins

• Transmembrane surface receptor binds signal molecule • Conformational change allows binding of G protein on cytoplasmic side • G protein binds GTP, becomes activated • G protein activates intracellular signal cascade

• Change in gene expression • Secrection • Many other possible consequences

10.2 Communicating junctions

• Gap junctions • animals • small molecules and ions may pass

• Plasmodesmata • plants • lined with plasma membrane • permit passage of water, sugars, etc.

10.2.1 Gap junctions

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.

11 Energy and Metabolism

11.1 Energy

• The capacity to do work. • Kinetic energy: energy of motion (ex. jogging). • Potential energy: stored energy (ex. a lion that is about to leap on its prey).

• Many forms of energy: e.g., • Heat • Sound • Electric current • Light • All convertible to heat

• Most energy for biological world is from sun • Heat (energy of random molecular motion, thermal energy)

• Convenient in biology • All other energy forms can be converted to heat • Thermodynamics: study of thermal energy

• Heat typically measured in kilocalories • Kcal: 1000 calories • 1 calorie: amount of heat required to raise the temperature of one gram of water one

degree Celsius (°C) • Heat plays major role in biological systems

• Ecological importance • Biochemical reactions

11.2 Oxidation–Reduction

• Energy flows into biological world from sun • Light energy is captured by photosynthesis

• Light energy raises electrons to higher energy levels • Stored as potential energy in covalent C-H bonds of sugars

• Strength of covalent bond is measured by amount of energy required to break it • 98.8 kcal/mole of C-H bonds

• In chemical reaction, energy stored in covalent bonds may transfer to new bonds. When this involves transfer of electrons, it is oxidation–reduction reaction

• Always take place together • Electron lost by atom or molecule through oxidation is gained by another atom or

molecule through reduction • Potential energy is transferred from one molecule to another (but never 100%)

Energy and Metabolism

• Often called redox reactions • Photosynthesis • Cellular Respiration • Chemiosynthesis • Autotrophs • Heterotrophs

11.3 NAD+

• Common electron acceptor/donor in redox reactions • Energetic electrons often paired with H+

11.4 Free energy

• Energy required to break and subsequently form other chemical bonds • Chemical bonds: sharing of electrons, tend to hold atoms of molecule together • Heat, by increasing atomic motion, makes it easier to break bonds (entropy)

• Energy available to do work in a system • In cells, G = H - TS

• G = Gibbs’ free energy • H = H (enthalpy) energy in molecule’s chemical bonds • TS (T, temperature in °K; S, entropy)

• Chemical reactions break and make bonds, producing changes in energy • Under constant conditions of temperature, pressure and volume, ∆G = ∆H - T∆S • ∆G, change in free energy

• If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction, does not proceed spontaneously; require input of energy (e.g., heat)

• If negative (–), H is lower, S is higher. Product has less free energy; exergonic; spontaneous

===Activation energy = ==

• Reactions with –∆G often require activation energy • e.g., burning of glucose • Must break existing bonds to get reaction started

• Catalysts lower activation energy

11.5 Enzymes

• Biological catalysts • Protein • RNA (ribozyme)

• Stabilizes temporary association between reactants (substrates) to facilitate reaction • Correct orientation • Stressing bonds of substrate

Enzymes

• Lower activation energy • Not consumed (destroyed) in reaction

11.5.1 Carbonic anhydrase

• Important enzyme of red blood cells • CO2 + H2O → H2CO3 -> HCO3 + H+ • Carbonic anhydrase catalyzes 1st reaction

• Converts water to hydroxyl • Orients the hydroxyl and CO2

11.5.2 Enzyme mechanism

• One or more active sites which bind substrates (reactants) • Highly specific

• Binding may alter enzyme conformation, inducing better fit

11.5.3 Factors affecting enzyme activity

• Substrate concentration • Product concentration • Cofactor concentration • Temperature • pH • Inhibitors

• Competitive: bind to active site • Noncompetitive: bind to 2nd site, called allosteric site; changes enzyme conformation

• Activators • Bind to allosteric sites, increase enzyme activity

Cofactors

• Required by some enzymes • Positively charged metal ions

• e.g., ions of Zn1, Mo, Mg, Mn • Draw electrons away from substrate (stress chemical bonds)

• Non-protein organic molecules (coenzymes) • E.g., NAD+, NADP+, etc. • Major role in oxidation/reduction reactions by donating or accepting electrons

1 http://en.wikibooks.org/wiki/Zinc

http://en.wikibooks.org/wiki/Zinc
Energy and Metabolism

11.6 ATP

• Adenosine triphosphate • Major energy currency of cells, power endergonic reactions • Stores energy in phosphate bonds

• Highly negative charges, repel each other • Makes these covalent bonds unstable

• Low activation energy • When bonds break, energy is transferred • ATP → ADP + Pi + 7.3 kcal/mole

11.7 Biochemical pathways

• Metabolism: sum of chemical reactions in cell/organism • Many anabolic and catabolic reactions occur in sequences (biochemical pathways) • Often highly regulated

Evolution of biochemical pathways

• Protobionts or 1st cells likely used energy rich substrates from environment • Upon depletion of a substrate, selection would favor catalyst which converts another

molecule into the depleted molecule • By iteration, pathway evolved backward

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.

12 Respiration: harvesting of energy

Glucose + O2 → CO2 + H2O + ATP

12.1 Energy

• Energy is primarily in C-H bonds (C-O too) • Chemical energy drives metabolism

• Autotrophs: harvest energy through photosynthesis or related process (plants, algae, some bacteria)

• Heterotrophs: live on energy produced by autotrophs (most bacteria and protists, fungi, animals)

• Digestion: enzymatic breakdown of polymers into monomers • Catabolism: enzymatic harvesting of energy • Respiration: harvesting of high energy electrons from glucose

12.2 Respiration

• Transfer of energy from high energy electrons of glucose to ATP • Energy depleted electron (with associated H+) is donated to acceptor molecule

• Aerobic respiration: oxygen accepts electrons, forms water • Anaerobic respiration: inorganic molecule accepts hydrogen/electron • Fermentation: organic molecule accepts hydrogen/electron

12.3 Respiration of glucose

• C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy • ∆G = -720 kcal/mole under cellular conditions • Largely from the 6 C-H bonds • Same energy whether burned or catabolized • In cells, some energy produces heat, most is transferred to ATP

12.4 Alternative anaerobic respiration

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