GeneralBiology
General Biology
March 15, 2013
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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
Contents
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
IV
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
V
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