Chapter 5 Introduction to Nanobiology

2 Chapter 5 Biological Molecules: Components of the Molecular Machinery of Life Structural Hierarchy in Biology Viewed from the Bottom-Up Biological Function at the Nanoscale Practical Applications

| SectionChapter Section 1: Biological Molecules: Components of the Molecular Machinery of Life Introduction to Nanobiology 15 3 Molecular Machines The Biological Importance of Water The Building Blocks of DNA: Nucleotides Multifunctional Polymers: Proteins Lipids Carbohydrates The Bonds of Molecular Components

| SectionChapter Molecular Machines Biological Molecules: Components of the Molecular Machinery of Life 15 4

| SectionChapter Flagellar Motors Biological Molecules: Components of the Molecular Machinery of Life 15 5

| SectionChapter The Biological Importance of Water 6 Biological Molecules: Components of the Molecular Machinery of Life 15 Liquid Water Ice

| SectionChapter Single Stranded DNA Biological Molecules: Components of the Molecular Machinery of Life 15 7

| SectionChapter DNA: Watson-Crick Base Pairs Biological Molecules: Components of the Molecular Machinery of Life 15 8

| SectionChapter Single Stranded RNA Biological Molecules: Components of the Molecular Machinery of Life 15 9

| SectionChapter Multifunctional Polymers: Proteins Biological Molecules: Components of the Molecular Machinery of Life 15 10

| SectionChapter Phospholipids Biological Molecules: Components of the Molecular Machinery of Life 15 11

| SectionChapter Biological Molecules: Components of the Molecular Machinery of Life 15 Self Assembling Monolayer Membrane 12

| SectionChapter Common Sugars – C n (H 2 O) n Biological Molecules: Components of the Molecular Machinery of Life 15 13

| SectionChapter Glucose Biological Molecules: Components of the Molecular Machinery of Life 15 14

| SectionChapter Carbohydrates: Glucose Polymers Biological Molecules: Components of the Molecular Machinery of Life 15 glycogen linear: α (1 → 4) D-glucose branch: α (1 → 6) D-glucose cellulose linear: β (1 → 4) D-glucose 15

| SectionChapter Ribose Biological Molecules: Components of the Molecular Machinery of Life 15 16

| SectionChapter Nucleic Acids Biological Molecules: Components of the Molecular Machinery of Life 15 DNARNA 17

| SectionChapter The Bonds of Molecular Components polymermonomeratoms nucleic acids DNA RNA 4 nucleotides ( G C A T ) 4 nucleotides ( G C A U ) C H N O P linear; A-helix linear proteins20 D amino acidsC H N O Slinear carbohydratesC n (H 2 O) n n: 5, 6C H Olinear, branched phospholipidsC H N O Pmonolayer, bilayer waterH Ohydrogen bonded network Biological Molecules: Components of the Molecular Machinery of Life 15 18

| SectionChapter Section 2: Structural Hierarchy in Biology Viewed from the Bottom-Up Introduction to Nanobiology Learning from Nature Structures within Structures: DNA Complexity and Diversity of Structured Components: Proteins Other Structures within Structures: Cells Structures within Cells: Phospholipids Inner Components of Cells: Organelles Origin of Color in Biology: Chemical or Structural? Physical Characteristics Bottom-Up Hierarchy

| SectionChapter Learning from Nature Structural Hierarchy in Biology Viewed from the Bottom-Up 25 20

| SectionChapter Structures within Structures: DNA Structural Hierarchy in Biology Viewed from the Bottom-Up 25 21

| SectionChapter Scaffolded DNA Origami Structural Hierarchy in Biology Viewed from the Bottom-Up 25 22

| SectionChapter Complexity and Diversity of Proteins Structural Hierarchy in Biology Viewed from the Bottom-Up Primary Protein StructureSecondary Protein Structure Quaternary Protein StructureTertiary Protein Structure

| SectionChapter Protein Folding Structural Hierarchy in Biology Viewed from the Bottom-Up 25 24

| SectionChapter Collagen Self-Assembly Structural Hierarchy in Biology Viewed from the Bottom-Up 25 25

| SectionChapter Other Structures within Structures: Cells Structural Hierarchy in Biology Viewed from the Bottom-Up 25 26

| SectionChapter Other Structures within Structures: Cells Structural Hierarchy in Biology Viewed from the Bottom-Up 25

| SectionChapter Inner Components of Cells: Organelles Structural Hierarchy in Biology Viewed from the Bottom-Up Nucleus −DNA storage and gene expression Mitochondria −Energy conversion: glucose bonds to ATP bonds Chloroplasts −Energy conversion: sunlight to ATP bonds Endoplasmic Reticulum −Synthesis and transport processes Golgi Apparatus −Synthesis and transport processes

| SectionChapter Structures within Cells: Phospholipids Structural Hierarchy in Biology Viewed from the Bottom-Up 25 29

| SectionChapter Structures within Cells: Phospholipids Structural Hierarchy in Biology Viewed from the Bottom-Up 25 30

| SectionChapter Origin of Color in Biology: Chemical or Structural? 31 South American Butterfly from Genus Morpho −Tops of brown wings appear iridescent blue −Photonic structures Constructive interference from Stacked chitin lamellae (~70 nm) Structural Hierarchy in Biology Viewed from the Bottom-Up 25 False color SEM image, X14,000

| SectionChapter Origin of Color in Biology: Chemical or Structural? 32 Structural Hierarchy in Biology Viewed from the Bottom-Up 25 Blue-Ringed Octopus −Hapalochlaena lunulata Dynamic Photonic Structure −~70 nm Bragg reflector with adjustable spacing

| SectionChapter Physical Characteristics Structural Hierarchy in Biology Viewed from the Bottom-Up ± 1º153 ± 1º Biomimetic Silanized Silicon SurfaceLotus Leaf 33

| SectionChapter Bottom-Up Hierarchy 34 Biological Molecules Cells Tissues Organisms Populations and Communities Ecosystems Biosphere Structural Hierarchy in Biology Viewed from the Bottom-Up 25

| SectionChapter Section 3: Biological Function at the Nanoscale Introduction to Nanobiology Processes of DNA −Reproduction of genetic information −Gene expression and RNA Energy Production for Cell Use −Transportation of materials for energy production −Cross-membrane energy production and storage −Energy production through sunlight conversion Energy Processes as Motors −Nanomotors Cell and Environment Interaction

| SectionChapter Gene Expression and RNA 36 Biological Function at the Nanoscale 35

| SectionChapter Reproduction of Genetic Information 37 Biological Function at the Nanoscale 35

| SectionChapter Energy Production for Cell Use 38 Biological Function at the Nanoscale 35

| SectionChapter Transportation of Materials for Energy Production 39 Biological Function at the Nanoscale 35  empty binding site T ATP D ADP P P i

| SectionChapter Cross-Membrane Energy Production and Storage 40 Biological Function at the Nanoscale 35 3 Na + cytosol + 2 K + out + ATP → 3 Na + out + 2 K + cytosol + ADP + P i

| SectionChapter Cross-Membrane Energy Production and Storage 41 Biological Function at the Nanoscale 35

| SectionChapter Energy Production through Sunlight Conversion 42 Biological Function at the Nanoscale 35 3 H + lumen + ADP + P i → 3 H + stroma + ATP Matrix/Stroma Intermembrane Space/Lumen

| SectionChapter Energy Processes as Motors 43 Biological Function at the Nanoscale 35

| SectionChapter Nanomotors 44 Biological Function at the Nanoscale 35 Biomimetic Nanomotor Requirements −Energy source −Unidirectional, 360º rotation Biomotor Predictions −0.05 to 0.2 rotations per picosecond Mixotricha Paradoxa, a Cellulose-Digesting Protozoan that Inhabits Termite Guts −Translocation from symbiotic bacterial colony

| SectionChapter Cell and Environment Interaction 45 Biological Function at the Nanoscale 35 Dynamic Focal Adhesion Complex Integrin Surface Proteins ECM Recognition Site: RGD

| SectionChapter Section 4: Practical Applications Introduction to Nanobiology DNA Sequencing Detection and Diagnostics DNA Microarrays Protein Microarrays Detection Using Nanoparticles Materials Delivery System Creating Compatible Artificial Surfaces Creating Tissues Out of Cells Looking Ahead

| SectionChapter DNA Sequencing 47 Practical Applications 45 ConventionalNanotechnology Concept

| SectionChapter Detection and Diagnostics 48 Practical Applications 45 Enzyme-Linked Immunosorbent Assay (ELISA) Immuno-PCR Bio-Barcode Assay

| SectionChapter Microarrays 49 Practical Applications 45 Protein Microarrays DNA Microarrays

| SectionChapter Detection Using Nanoparticles 50 Practical Applications 45 Visualization −Quantum dots Targeted Delivery −Magnetic or optically activated nanoparticles

| SectionChapter Materials Delivery System 51 Practical Applications 45 Giant Unilamellar Vesicle Liposomal Gene Delivery Vesicles

| SectionChapter Creating Compatible Artificial Surfaces 52 Practical Applications 45

| SectionChapter Looking Ahead 53 Practical Applications 45 When Might We See: −Transplantable tissues created from cells? −Organ replacement via tissue engineering? −Life be created by directed assembly of molecular systems?