Taking a system approach to expose modern biology, this book presents the fundamental system principles and parameters common to all living species. The straightforward examination begins with a presentation of molecular cell biology and progresses to the complex interrelationship between genes and proteins as observed in metabolic process, signal transduction, cell division and embryonic development. The book's unique approach provides a depiction of the human genome project, a review of high throughput biology and bioinformatic tools and a presentation of gene circuitry and pathway analysis as applied to cell division, development of embryo and metabolic pathways and expose of emerging proteomic science.The volume presents the chemistry of life, macromolecules of life, cells and their housekeeping functions, gene circuits, genomics, cell adhesion and communication, cell division and its regulation, development of multicellular organisms and large scale biology.For computer scientists, physicists, and engineers.

Preface

xi

The Chemistry of Life

1

(31)

Introduction

1

(1)

Atoms

2

(4)

Molecules and Covalent Bonds

6

(7)

Ionic Compounds and Electrostatic Bonds

13

(1)

Water and Hydrogen Bonds

14

(1)

Lipids and van der Waals Attraction

15

(1)

Acids and Bases

16

(1)

Chemical Reactions

17

(7)

Enzymes

24

(3)

More on Bioelements

27

(2)

Assignments

29

(3)

References

31

(1)

Macromolecules of Life

32

(39)

Introduction

32

(4)

Fundamentals

36

(4)

Carbohydrates

40

(4)

Lipids

44

(3)

DNA and RNA

47

(10)

Proteins

57

(5)

The Genetic Code

62

(2)

Protein Structure and Function

64

(3)

Assignments

67

(4)

References

70

(1)

Cells and Their Housekeeping Functions

71

(43)

Introduction

71

(1)

Prokaryotes and Eukaryotes

72

(2)

Nucleus

74

(3)

Organelles for Protein Synthesis and Transport

77

(5)

Cytoskeleton

82

(4)

Metabolic Processes and Mitochondria

86

(12)

Molecular Motors

98

(6)

Cell Membrane

104

(3)

Active Membrane Transport

107

(4)

Assignments

111

(3)

References

113

(1)

Gene Circuits

114

(22)

Introduction

114

(1)

Gene to Protein

115

(3)

Gene Anatomy

118

(4)

Gene Circuits

122

(6)

Bionetworks

128

(3)

Assignments

131

(5)

References

134

(2)

Genomics: The Technology behind the Human Genome Project

136

(32)

Introduction

136

(1)

History of the Genome

137

(2)

Sequence Similarity and Homologous Genes

139

(5)

Decoding the Human Genome

144

(3)

Cutting and Sizing DNA

147

(3)

Making Multiple Copies

150

(7)

Sequencing

157

(3)

Gene Annotation

160

(3)

Plants and Animals with Modified Genomes

163

(1)

Assignments

164

(4)

References

166

(2)

Cell Adhesion and Communication

168

(24)

Introduction

168

(1)

Modes of Cell Communication

168

(2)

Extracellular Matrix (ECM) and Integrins

170

(5)

Cell-Cell Adhesion and Cadherins

175

(3)

Examples from Signal Transduction Pathways

178

(8)

Crosstalk between Signal Transduction Pathways

186

(5)

Assignments

191

(1)

References

191

(1)

Cell Division and Its Regulation

192

(23)

Introduction

192

(1)

Modes of Cell Division

193

(1)

Molecular Basis of Cell Division

194

(5)

Cell-Cycle Check Points

199

(1)

Phases of the Cell Cycle

200

(10)

Cell Culture

210

(2)

Assignments

212

(3)

References

214

(1)

Development of Multicellular Organisms

215

(25)

Introduction

215

(1)

From Unfertilized Egg to Zygote

216

(4)

Cleavage: First Stage of Development

220

(3)

Gastrulation

223

(5)

Pattern-Generating Genes

228

(6)

Stem Cells and Tissue Engineering

234

(3)

Assignments

237

(3)

References

238

(2)

Large-Scale Biology

240

(20)

Introduction

240

(1)

Microarrays

241

(3)

Proteomics

244

(8)

Protein Structure

252

(5)

Systems Biology

257

(1)

Assignments

258

(2)

References

259

(1)

Glossary

260

(16)

Index

276

What is included with this book?

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The Used, Rental and eBook copies of this book are not guaranteed to include any supplemental materials. Typically, only the book itself is included. This is true even if the title states it includes any access cards, study guides, lab manuals, CDs, etc.

New Biology for Engineers and Computer Scientistsis an easy-to-read modern biology book specifically targeting engineers, engineering students, and computer scientists. Biology is probably the most fascinating science of our time and is extraordinarily ambitious because it seeks to uncover the mysteries of life itself. Recent advances in biotechnology have already enabled scientists to decode the human genome. Considerable progress has also been made in understanding the complex world of proteins, and the networks they form within and across living cells. The systemwide analyses used in the New Biology era represent a paradigm shift for scientists accustomed to investigating discrete pathways or simple biological phenomena. The contribution of computer scientists and engineers to New Biology is undeniable. Genome sequencing and gene prediction are based on sophisticated pattern recognition analyses and the recent advances in nanotechnology and microrobotics have transformed proteomics from science fiction into reality. The exciting new integration of biology, physics, and computational sciences brings to light the need for a new type of engineer, one with a grasp of modern biology. Educating engineers in molecular cell biology has always been a challenge. Biology is perceived by many engineering students as a memorization, not a learning, class. However, New Biology is intellectually stimulating and can be mathematically rigorous; therefore, it has great appeal for engineers and computer scientists.New Biology is terminology rich, because researchers have identified many of the genes and proteins more or less arbitrarily. In addition, the procedures biologists use originate from a large variety of disciplines and are difficult to capture in a one-year course. As a result, most biology books are large, complex texts covering many topics such as the structure and function of cells, heredity, evolution, biology of plants and animals, and ecology and biogeography. As such, they are extremely useful learning tools for graduate students with a background in biology. On the other hand,New Biology for Engineers and Computer Scientistsfocuses narrowly on what we perceive to be the essentials of New Biology, namely, genes and proteins, cells as the basic units of life, cell division, and animal development.The contents ofNew Biology for Engineers and Computer Scientistsreflect the opinions voiced in an extensive survey among the biomedical engineering faculty in the United States. The survey also attested to the strong need for such a book.New Biology for Engineers and Computer Scientistsintroduces cells as robust complex networks of genes and proteins and adopts a systems view to discuss communication of cells with other cells and with the external environment. Some of the assignments listed at the end of each chapter illustrate the link between biology and engineering. In keeping with the "hands on" approach common in engineering classes, these assignment sections are a particularly important aspect of the learning experience ofNew Biology for Engineers and Computer Scientists.By completing the assignments, the student can both test his or her knowledge and expand it to include areas not covered directly in the text.New Biology for Engineers and Computer Scientistsintegrates the tools of bioinformatics throughout the text and illustrates their effective use: The assignments that follow are used to further emphasize the important themes of New Biology. These assignments typically have more specifics than the main text and refer the reader for further bioinformatics research to Web sites such as www.ncbi.nim.nih.gov/ and http://www.genome.ad.jp/dbget.html. Students will learn how to read nucleotide sequences from the Gene Bank, search for similarities among proteins or genes, and learn how to read molecular pathway diagrams.New Biology for Engineers and Computer Scientists