Biology for non-biologists
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1 Biology for non-biologists askabiologist.asu.edu Roisin Owens Associate Professor, Dept. Of Bioelectronics
2 The biologist and the engineer should be friends 2 Department of Bioelectronics
3 Outline Basics: individual molecules: DNA, RNA, proteins, lipids, sugars, proteins Elements of the cell; plasma membrane, nucleus (transcription), ribosome (translation), Elements of the cell contd.; cytoskeleton, mitochondria (energy) transport, cell division Cell types and function; neurons, epithelial cells, muscle cells, blood cells,
4 Questionnaire What do you know about biology? What is DNA where is it found? What is a protein? Give an example What is a tissue What is the difference between a eukaryote and a prokaryote Name 3 cell types What is a key property of a neuron?
5 Bibliography Biochemistry by Jeremy M. Berg ISBN Molecular Biology of the Cell 5 E by Bruce Alberts ISBN Principles of Anatomy and Physiology by Gerard J. Tortura ISBN
6 Some light reading The emperor of all maladies, Siddhartha Mukherjee The immortal life of Henrietta Lacks, Rebecca Skloot The dark lady of DNA, Brenda Maddox The red queen, Matt Ridley Power, Sex, Suicide, Nick Lane The Spark of Life, Frances Ashcroft
7 Levels of organisation in animal physiology 1. Whole organism 2. Tissue 3. Cells 4. Macromolecular structures 5. Single molecules
8 Comparison of Eukaryotic and Prokaryotic Cells Image: k12station.blogspot.com/2006_08_01_archive.html
9 Miller and Urey (1953) How did it all begin? RNA world 9 Department of Bioelectronics
10 Simple Chemistry Figure 2-6 Molecular Biology of the Cell ( Garland Science 2008)
11 Simple Chemistry Figure 2-8a Molecular Biology of the Cell ( Garland Science 2008)
12 Macromolecules Figure 2-17 Molecular Biology of the Cell ( Garland Science 2008)
13 Macromolecules Figure 2-32 Molecular Biology of the Cell ( Garland Science 2008)
14 Sugars Figure 2-18 Molecular Biology of the Cell ( Garland Science 2008)
15 Lipids Figure 2-22 Molecular Biology of the Cell ( Garland Science 2008)
16 Nucleotides Figure 2-26 Molecular Biology of the Cell ( Garland Science 2008)
17 Amino acids Figure 2-24 Molecular Biology of the Cell ( Garland Science 2008)
18 18
19 Proteins Primary structure = order of amino acids in the protein chain
20 Proteins Anatomy of an amino acid
21 Proteins How to remember the 1 letter code A: alanine C: cysteine D: aspartate E: glutamate F: phenylalanine G: glycine H: histidine I: isoleucine K: lysine L: leucine M:methionine N: Asparagine P: Proline Q: Glutamine R: Arginine S: Serine T: Threonine W: Tryptophan
22 Proteins Figure 3-1 (part 2 of 2) Molecular Biology of the Cell ( Garland Science 2008)
23 Proteins Non-polar R-groups tend to be buried in the cores of proteins Myoglobin Blue = non-polar R-group Red = Heme 23
24 Proteins Primary sequence reveals important clues about a protein Evolution conserves amino acids that are important to protein structure and function across species. Sequence comparison of multiple homologs of a particular protein reveals highly conserved regions that are important for function. Clusters of conserved residues are called motifs -- motifs carry out a particular function or form a particular structure that is important for the conserved protein. motif DnaG E. coli...epnrllvvegymdvval... DnaG S. typ...epqrllvvegymdvval... DnaG B. subt...kqeravlfegfadvyta... gp4 T3...GGKKIVVTEGEIDMLTV... gp4 T7...GGKKIVVTEGEIDALTV... small hydrophobic large hydrophobic polar positive charge negative charge 24 : : : : * * * : :
25 Proteins Getting amino acid sequence
26 Proteins: techniques Figure 8-18a Molecular Biology of the Cell ( Garland Science 2008)
27 Proteins Secondary structure = local folding of residues into regular patterns
28 Proteins Figure 3-5 Molecular Biology of the Cell ( Garland Science 2008)
29 Proteins Figure 3-7a,b,c Molecular Biology of the Cell ( Garland Science 2008)
30 Proteins Figure 3-7d,e,f Molecular Biology of the Cell ( Garland Science 2008)
31 Proteins Tertiary structure = global folding of a protein chain
32 Protein stability Proteins Electrostatic forces Interactions of positive and negative charges Ionic interactions (ion pair/salt bridge) Dipole-dipole interactions e.g Van der Waals Very weak, but very numerous Hydrogen bonding kj/mol Hydrophobic forces Hydrophobic go in, hydrophillic out Disulfide bonds Between 2 SH groups (251kJ/mol)
33 Proteins Protein denaturation Low conformation stability => highly susceptible to denaturation Changes in temperature (Tm less than 1OO C) but small changes in folding result in almost total loss of 3D structure ph changes: Ionisation of side groups change changes H-bonding, charge distrib. Detergents: change hydrophobic interactions Organic substances: interfere with hydrophobic interactions (have their own interaction with water) Salts: can stabilise (raise Tm) Ils can be good Chaotropic agents: urea, Guanidinium increase solubility of nonpolar substances in water disrupt hydrobphobic interactions (expel water)
34 Proteins: motifs reused Figure 3-16 Molecular Biology of the Cell ( Garland Science 2008)
35 Proteins Figure 8-28 Molecular Biology of the Cell ( Garland Science 2008)
36 Proteins Quaternary structure = Higher-order assembly of proteins
37 Proteins Examples of other quaternary structures Tetramer Hexamer Filament SSB DNA helicase Recombinase Allows coordinated Allows coordinated DNA binding Allows complete DNA binding and ATP hydrolysis coverage of an extended molecule
38 Protein types Figure 3-23 Molecular Biology of the Cell ( Garland Science 2008)
39 Protein types: enzymes Figure 3-46 Molecular Biology of the Cell ( Garland Science 2008)
40 Protein types: enzymes Table 3-2 Molecular Biology of the Cell ( Garland Science 2008)
41 DNA Figure 4-5 Molecular Biology of the Cell ( Garland Science 2008)
42 DNA synthesis: 5 -> 3 Figure 5-3 Molecular Biology of the Cell ( Garland Science 2008)
43 DNA polymerase Figure 5-4 Molecular Biology of the Cell ( Garland Science 2008)
44 High fidelity DNA synthesis Table 5-1 Molecular Biology of the Cell ( Garland Science 2008)
45 DNA mutations Table 5-2 Molecular Biology of the Cell ( Garland Science 2008)
46 DNA amplification: PCR Figure 8-45a Molecular Biology of the Cell ( Garland Science 2008)
47 DNA to RNA Figure 6-2 Molecular Biology of the Cell ( Garland Science 2008)
48 RNA: ribonucleic acid Figure 6-4 Molecular Biology of the Cell ( Garland Science 2008)
49 RNA: ribonucleic acid Figure 6-4a Molecular Biology of the Cell ( Garland Science 2008)
50 RNA: ribonucleic acid Figure 6-4b Molecular Biology of the Cell ( Garland Science 2008)
51 RNA structures Figure 6-6 Molecular Biology of the Cell ( Garland Science 2008)
52 Transcription results in ss RNA Figure 6-7 Molecular Biology of the Cell ( Garland Science 2008)
53 Multiple types of RNA Table 6-1 Molecular Biology of the Cell ( Garland Science 2008)
54 RNA polymerase Figure 6-8a Molecular Biology of the Cell ( Garland Science 2008)
55 RNA synthesis Figure 6-17 Molecular Biology of the Cell ( Garland Science 2008)
56 RNA is exported Figure 6-39b Molecular Biology of the Cell ( Garland Science 2008)
57 Ribosomes are made in the nucleolus Figure 6-44a Molecular Biology of the Cell ( Garland Science 2008)
58 The genetic code Figure 6-50 Molecular Biology of the Cell ( Garland Science 2008)
59 Three reading frames Figure 6-51 Molecular Biology of the Cell ( Garland Science 2008)
60 The ribosome Figure 6-64 Molecular Biology of the Cell ( Garland Science 2008)
61 Translation: polyribosomes Figure 6-76 Molecular Biology of the Cell ( Garland Science 2008)
62 Ribosomes: targets for antibiotics Figure 6-79 Molecular Biology of the Cell ( Garland Science 2008)
63 Ribosomes: targets for antibiotics Table 6-4 Molecular Biology of the Cell ( Garland Science 2008)
64 The Cell Membrane Figure 10-1 Molecular Biology of the Cell ( Garland Science 2008)
65 Membrane proteins Figure 10-1b Molecular Biology of the Cell ( Garland Science 2008)
66 Single vs Double bonds saturated unsaturated Figure 2-9 Molecular Biology of the Cell ( Garland Science 2008)
67 Polar vs non-polar Figure 2-10 Molecular Biology of the Cell ( Garland Science 2008)
68 Hydrophobic vs hydrophillic Figure 10-6 Molecular Biology of the Cell ( Garland Science 2008)
69 Cell membrane lipids Figure 10-2 Molecular Biology of the Cell ( Garland Science 2008)
70 Membrane structure Figure 10-8 Molecular Biology of the Cell ( Garland Science 2008)
71 Membrane composition Table 10-1 Molecular Biology of the Cell ( Garland Science 2008)
72 Membrane asymmetry Figure 10-17a Molecular Biology of the Cell ( Garland Science 2008)
73 Membrane proteins Figure Molecular Biology of the Cell ( Garland Science 2008)
74 Membrane proteins Figure Molecular Biology of the Cell ( Garland Science 2008)
75 Membrane proteins + = hydrophobic - = hydrophillic Figure Molecular Biology of the Cell ( Garland Science 2008)
76 Membrane transport Figure 11-1 Molecular Biology of the Cell ( Garland Science 2008)
77 Membrane transport: transporters/channels Figure 11-3a Molecular Biology of the Cell ( Garland Science 2008)
78 Membrane transport Figure 11-4b Molecular Biology of the Cell ( Garland Science 2008)
79 Active transport Figure 11-7 Molecular Biology of the Cell ( Garland Science 2008)
80 Na + /K + pumps: for maintaining osmolarity Figure Molecular Biology of the Cell ( Garland Science 2008)
81 Eukaryotic cell structure stephenyardleybrendan.blogspot.com
82 Visualising cells Figure 9-2 Molecular Biology of the Cell ( Garland Science 2008)
83 Visualising cells: immunofluorescence Figure 9-18 Molecular Biology of the Cell ( Garland Science 2008)
84 Visualising cells: EM Figure 9-45 Molecular Biology of the Cell ( Garland Science 2008)
85 The cytoskeleton: organisation Figure 16-5 Molecular Biology of the Cell ( Garland Science 2008)
86 The cytoskeleton: rapid diss/assembly Figure 16-7 Molecular Biology of the Cell ( Garland Science 2008)
87 The cytoskeleton: filaments Figure 16-9 Molecular Biology of the Cell ( Garland Science 2008)
88 Microtubules Figure Molecular Biology of the Cell ( Garland Science 2008)
89 Actin Figure Molecular Biology of the Cell ( Garland Science 2008)
90 Other filaments Table 16-1 Molecular Biology of the Cell ( Garland Science 2008)
91 Actin arrays Figure Molecular Biology of the Cell ( Garland Science 2008)
92 Microvilli: actin bundle structure Figure 16-50a Molecular Biology of the Cell ( Garland Science 2008)
93 Molecular motors: actin based (myosin) Motor proteins can bind to polarised filaments (actin or MT) and use Energy to move along it Figure 16-54a Molecular Biology of the Cell ( Garland Science 2008)
94 Myosin in muscle Figure 16-55c Molecular Biology of the Cell ( Garland Science 2008)
95 Actin polymerisation dependent movement Figure Molecular Biology of the Cell ( Garland Science 2008)
96 Intracellular compartments Figure 12-1 Molecular Biology of the Cell ( Garland Science 2008)
97 Protein traffic: 3 types Figure 12-6 Molecular Biology of the Cell ( Garland Science 2008)
98 Vesicular traffic Figure 12-7 Molecular Biology of the Cell ( Garland Science 2008)
99 Signal sequences Table 12-3 Molecular Biology of the Cell ( Garland Science 2008)
100 Transport to the lysosome Page 779 Molecular Biology of the Cell ( Garland Science 2008)
101 Transport to the lysosome Figure Molecular Biology of the Cell ( Garland Science 2008)
102 Transport into the cell Figure Molecular Biology of the Cell ( Garland Science 2008)
103 Transport out of the cell Page 799 Molecular Biology of the Cell ( Garland Science 2008)
104 The Mitochondrion Figure 14-8 (part 1 of 2) Molecular Biology of the Cell ( Garland Science 2008)
105 Chemiosmotic coupling Figure 14-1 Molecular Biology of the Cell ( Garland Science 2008)
106 Electron transport chain Figure 14-3 Molecular Biology of the Cell ( Garland Science 2008)
107 Energy from food generates NADH Figure Molecular Biology of the Cell ( Garland Science 2008)
108 Biological systems store energy Figure 14-12a Molecular Biology of the Cell ( Garland Science 2008)
109 Oxidative phosphorylation Figure Molecular Biology of the Cell ( Garland Science 2008)
110 Generation of membrane potential Figure Molecular Biology of the Cell ( Garland Science 2008)
111 ATP synthase Figure Molecular Biology of the Cell ( Garland Science 2008)
112 ATP:ADP ratio is high Figure Molecular Biology of the Cell ( Garland Science 2008)
113 Energy yields Table 14-1 Molecular Biology of the Cell ( Garland Science 2008)
114 Mitochondria: key role in cell metabolism Figure Molecular Biology of the Cell ( Garland Science 2008)
115 The cell cycle Meiosis and Mitosis Figure Molecular Biology of the Cell ( Garland Science 2008)
116 The cell cycle Figure 17-1 Molecular Biology of the Cell ( Garland Science 2008)
117 The cell cycle Figure 17-4 Molecular Biology of the Cell ( Garland Science 2008)
118 The cell cycle: cyclins control checkpoints Figure Molecular Biology of the Cell ( Garland Science 2008)
119 Apoptosis: programmed cell death Figure 18-1 Molecular Biology of the Cell ( Garland Science 2008)
120 Apoptosis: during embryonic develop. Figure 18-2 Molecular Biology of the Cell ( Garland Science 2008)
121 Apoptosis: mediated by caspases Figure 18-5a Molecular Biology of the Cell ( Garland Science 2008)
122 Apoptosis: can be signalled from outside Figure 18-6 Molecular Biology of the Cell ( Garland Science 2008)
123 Apoptosis: can be signalled from mito. Figure 18-8 Molecular Biology of the Cell ( Garland Science 2008)
124 Cell types
125 Cell types Figure 8-5 Molecular Biology of the Cell ( Garland Science 2008)
126 Tissue culture
127 Cell Communication Figure 15-1 Molecular Biology of the Cell ( Garland Science 2008)
128 Extracellular receptors Figure 15-3a Molecular Biology of the Cell ( Garland Science 2008)
129 Intracellular receptors Figure 15-3b Molecular Biology of the Cell ( Garland Science 2008)
130 Types of signalling molecules Proteins Small peptides Amino acids Nucleotides Steroids Retinoids Fatty acid derivatives Dissolved gases (NO, CO)
131 Intercellular signalling Figure 15-4 Molecular Biology of the Cell ( Garland Science 2008)
132 Signalling can be slow or fast Figure 15-6 Molecular Biology of the Cell ( Garland Science 2008)
133 Cells selectively respond to signals Figure 15-8 Molecular Biology of the Cell ( Garland Science 2008)
134 A sample signalling pathway Figure Molecular Biology of the Cell ( Garland Science 2008)
135 Ca 2+ is a ubiquitous mediator Location Cytosol Extracellular fluid Ca 2+ concentration 10-7 M 10-3 M ER 10-4 M Egg fertilisation triggers Ca 2+ Figure Molecular Biology of the Cell ( Garland Science 2008)
136 Tissue types Four Types of Animal Tissue: 1. Epithelial/Barrier Tissue Covers body surfaces and lines organs, cavities and ducts, glands too 2. Connective Tissue Protects and supports. Bind organs, stores energy as fat, helps provide immunity 3. Muscle Tissue Generates physical force to make body move and generates body heat 4. Nervous Tissue Detects changes in environment inside and out and responds by generating action potentials that activate muscle contractions and secretions
137 Cell junctions, adhesions and ECM Figure 19-1 Molecular Biology of the Cell ( Garland Science 2008)
138 Cell junctions Figure 19-2 Molecular Biology of the Cell ( Garland Science 2008)
139 Cell junctions Figure 19-3 Molecular Biology of the Cell ( Garland Science 2008)
140 Basal lamina /basement membrane Figure Molecular Biology of the Cell ( Garland Science 2008)
141 ECM molecules Figure Molecular Biology of the Cell ( Garland Science 2008)
142 Model of basal lamina Figure Molecular Biology of the Cell ( Garland Science 2008)
143 ECM molecules: integrins Figure Molecular Biology of the Cell ( Garland Science 2008)
144 Integrin mediated T cell activation Figure Molecular Biology of the Cell ( Garland Science 2008)
145 Adhesion molecule summary Table 19-5 Molecular Biology of the Cell ( Garland Science 2008)
146 Connective tissue Figure Molecular Biology of the Cell ( Garland Science 2008)
147 Connective tissue: hydrogels Glycosaminoglycans: Hyaluronic acid Chondroitin sulfate Dermatan sulfate Heparan sulfate Keratan sulfate Figure Molecular Biology of the Cell ( Garland Science 2008)
148 Neurons Figure Molecular Biology of the Cell ( Garland Science 2008)
149 Neurons Figure 11-35a Molecular Biology of the Cell ( Garland Science 2008)
150 Neuromuscular junction Figure Molecular Biology of the Cell ( Garland Science 2008)
151 Synapses require complex adhesion Figure 19-22c Molecular Biology of the Cell ( Garland Science 2008)
152 Cellular Diversity The average adult has nearly 100 trillion cells There are about 200 different types of cells Cells come in a variety of shapes and sizes Cellular diversity permits organization of cells into more complex tissues and organs Copyright 2009 John Wiley & Sons, Inc.
153 What is a Tissue? A tissue is a group of cells Common embryonic origin Function together to carry out specialized activities Hard (bone), semisolid (fat), or liquid (blood) Histology is the science that deals with the study of tissues. Pathologist specialized in laboratory studies of cells and tissue for diagnoses Copyright 2009 John Wiley & Sons, Inc.
154 Tissues as building blocks of organ systems Human body 10 major organ systems Each organ (e.g., lung) Functional units (e.g., alveoli) Tissues
155 Epithelial Tissues Epithelial tissue consists of cells arranged in continuous sheets, in either single or multiple layers Closely packed and held tightly together Covering and lining of the body Free surface 3 major functions: Selective barrier that regulates the movement of materials in and out of the body Secretory surfaces that release products onto the free surface Protective surfaces against the environment Copyright 2009 John Wiley & Sons, Inc.
156 General Features of Epithelial Cells Basement membrane Thin double extracellular layer that serves as the point of attachment and support for overlying epithelial tissue Basal lamina Closer to and secreted by the epithelial cells Contains laminin, collagen, glycoproteins, and proteoglycans Reticular lamina Closer to the underlying connective tissue Contains collagen secreted by the connective tissue cells Copyright 2009 John Wiley & Sons, Inc.
157 Connective tissue Figure Molecular Biology of the Cell ( Garland Science 2008)
158 Connective Tissue Most abundant and widely distributed tissues in the body Numerous functions Binds tissues together Supports and strengthen tissue Protects and insulates internal organs Compartmentalize and transport Energy reserves and immune responses Copyright 2009 John Wiley & Sons, Inc.
159 Liquid Connective Tissue Blood tissue Connective tissue with liquid extracellular matrix called blood plasma Lymph Copyright 2009 John Wiley & Sons, Inc.
160 Blood cells Figure Molecular Biology of the Cell ( Garland Science 2008)
161 Muscular Tissue Consists of elongated cells called muscle fibers or myocytes Cells use ATP to generate force Several functions of muscle tissue Classified into 3 types: skeletal, cardiac, and smooth muscular tissue
162 Nervous Tissue Consists of two principle types of cells Neurons or nerve cells Neuroglia Copyright Institut 2009, Mines-Télécom John Wiley & Sons, Inc.
163 Excitable Cells Neurons and muscle fibers Exhibit electrical excitability The ability to respond to certain stimuli by producing electrical signals such as action potentials Actions potentials propagate along a nerve or muscle plasma membrane to cause a response Release of neurotransmitters Muscle contraction Copyright 2009, John Wiley & Sons, Inc.
164 Outline Basics: individual molecules: DNA, RNA, proteins, lipids, sugars, proteins Elements of the cell; plasma membrane, nucleus (transcription), ribosome (translation), Elements of the cell contd.; cytoskeleton, mitochondria (energy) transport, cell division Cell types and function; neurons, epithelial cells, muscle cells, blood cells,
Components of a functional cell. Boundary-membrane Cytoplasm: Cytosol (soluble components) & particulates DNA-information Ribosomes-protein synthesis
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