About the EditorsWilliam V. Dashek, Emeritus Professor, Mary Baldwin College, USA Dr. Dashek is the recipient of BS, MS and Ph.D. degree from Marquette University where he was a National Institute of Health pre-doctoral trainee. He was a post-doctorate fellow at the Michigan State University Plant research Laboratory. Subsequently, he began a lengthy Academic teaching and research career. Currently, Dashek is retired writing advanced textbooks. Gurbachan S. Miglani, Visiting Professor, School of Agricultural Biotechnology, Punjab Agricultural University, IndiaDr. Miglani obtained B.Sc. (Agri. & A.H.) and M.Sc. (Genetics) from Punjab Agricultural University (PAU), Ludhiana, Punjab, India and Ph.D. from Howard University, Washington, D.C. During his 35-year teaching stint at PAU he taught general and specialized courses in genetics. Even after retirement Miglani is still teaching molecular genetics and biotechnology at PAU. In addition to research and review papers, popular science articles, laboratory manuals he has published a dozen books and presently he is writing his next book.

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• Contributors ixPreface xiAcknowledgments xii1 An introduction to cells and their organelles 1William V. DashekCells 1Cell organelles – an introduction 6Ion channels 10Proton pumps 14Water channels 14Carriers 15Cell death 17References 18Further reading 242 Isolation and characterization of subcellular organelles from plant cells 25Milee Agarwal, P. Desai, and Harish PadhIsolation of subcellular organelles 26Identification and characterization of isolated organelles 33Summary 39References 39Further reading 413 Endoplasmic reticulum 42William V. DashekStructure 42Chemical composition 42Biogenesis 45Functions 45Posttranslational events 49Inhibitors 53In vitro protein synthesis 54Other functions 54References 54Further reading 604 The Golgi apparatus 61D. Davis, T.E. Wilkop, and Georgia DrakakakiThe Golgi apparatus 61Plant Golgi introduction 66Structure and organization 69Golgi‐mediated vesicular trafficking 71Plant Golgi‐dependent cellular processes 74Imaging and visualization 76Isolation and analysis 78Golgi genetics and genomics 81Significance 84Acknowledgment 85References 85Further reading 875 Microbodies 88Robert DonaldsonIntroducing peroxisomes 88Leaf peroxisomes 89Peroxisomes in oil seeds and pollen 91References 107Further reading 1096 Microtubules, intermediate filaments, and actin filaments 110William V. DashekMicrotubules 110Intermediate filaments 113Actin filaments (microfilaments) 116References 119Further reading 1247 The mitochondrion 125Ray J. Rose, Terence W.‐Y. Tiew, and William V. DashekStructure and dynamics 125The mitochondrial genome 128Comparison of the mitochondrial genome with chloroplast and nuclear genomes 131The mitochondrial proteome and protein import 132Respiratory metabolite transporters 133The electron transport chain and oxidative phosphorylation 133The alternative electron transfer chain in plant mitochondria 139Plant mitochondria, stress responses and programmed cell death 139Other functions of plant mitochondria 140References 144Further reading 1458 Nucleus 146Yogesh Vikal and Dasmeet KaurStructural organization of the NE 147Nuclear pores 152The nucleolus 157Chromatin and chromosomes 165DNA structure 170DNA replication 173RNA structure, function, and synthesis 176Nucleocytoplasmic transport, nuclear import, and nuclear export 183The dynamics of NE biogenesis during mitosis 188The dynamics of nuclear pore complex biogenesis 196Cell cycle control 200Summary 205References 206Further reading 2079 Plant cell walls 209James E. Bidlack and William V. DashekIntroduction 209Structure 209Biosynthesis 216Chemical composition 217Biogenesis 222Function 225References 231Further reading 23810 Plastid structure and genomics 239Gurbachan S. MiglaniPlastid structure 239Different forms of plastids 240Plastid stromules 248Chlorophyll biosynthesis 248Plastid genomics 250Sequenced plastomes 253Promiscuous DNA 258Plastid genome organization 260Plastid gene organization, expression, and regulation 265Systems biology approach in understanding chloroplast development 269Chloroplast genetic engineering 284Recent trends in chloroplast research 289Summary 293References 294Further reading 29911 Photosynthesis 300J. Kenneth HooberIntroduction 300Evolution of photosynthesis 301Development of the chloroplast 310Absorption of light energy 317Generation of end products 324Distribution of the photosystems in thylakoid membranes 329Photoinhibition: damage and repair of the PS II reaction center 332Protection of PS II by carotenoids 332Incorporation of carbon as CO2 into carbohydrate 334End products of carbon assimilation 346Conclusions for the reactions of photosynthesis 348References 348Further reading 35012 Vacuoles and protein bodies 351William V. Dashek and Amy M. CloreVacuoles 351PBs and other protein storage compartments 359References 365Further reading 37013 Systems biology in plant cells and their organelles 371Rajdeep Kaur Grewal, Saptarshi Sinha, and Soumen RoySystems biology—“omics” 371Genomics 373Lipidomics 378Metabolomics 380Proteomics 382Transcriptomics 384Synthetic biology 386Acknowledgments 388References 389Further reading 391Appendix A 392Appendix B 400Appendix C 403Index 407

About the EditorsWilliam V. Dashek, Emeritus Professor, Mary Baldwin College, USA Dr. Dashek is the recipient of BS, MS and Ph.D. degree from Marquette University where he was a National Institute of Health pre-doctoral trainee. He was a post-doctorate fellow at the Michigan State University Plant research Laboratory. Subsequently, he began a lengthy Academic teaching and research career. Currently, Dashek is retired writing advanced textbooks. Gurbachan S. Miglani, Visiting Professor, School of Agricultural Biotechnology, Punjab Agricultural University, IndiaDr. Miglani obtained B.Sc. (Agri. & A.H.) and M.Sc. (Genetics) from Punjab Agricultural University (PAU), Ludhiana, Punjab, India and Ph.D. from Howard University, Washington, D.C. During his 35-year teaching stint at PAU he taught general and specialized courses in genetics. Even after retirement Miglani is still teaching molecular genetics and biotechnology at PAU. In addition to research and review papers, popular science articles, laboratory manuals he has published a dozen books and presently he is writing his next book.

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• Contributors ixPreface xiAcknowledgments xii1 An introduction to cells and their organelles 1William V. DashekCells 1Cell organelles – an introduction 6Ion channels 10Proton pumps 14Water channels 14Carriers 15Cell death 17References 18Further reading 242 Isolation and characterization of subcellular organelles from plant cells 25Milee Agarwal, P. Desai, and Harish PadhIsolation of subcellular organelles 26Identification and characterization of isolated organelles 33Summary 39References 39Further reading 413 Endoplasmic reticulum 42William V. DashekStructure 42Chemical composition 42Biogenesis 45Functions 45Posttranslational events 49Inhibitors 53In vitro protein synthesis 54Other functions 54References 54Further reading 604 The Golgi apparatus 61D. Davis, T.E. Wilkop, and Georgia DrakakakiThe Golgi apparatus 61Plant Golgi introduction 66Structure and organization 69Golgi‐mediated vesicular trafficking 71Plant Golgi‐dependent cellular processes 74Imaging and visualization 76Isolation and analysis 78Golgi genetics and genomics 81Significance 84Acknowledgment 85References 85Further reading 875 Microbodies 88Robert DonaldsonIntroducing peroxisomes 88Leaf peroxisomes 89Peroxisomes in oil seeds and pollen 91References 107Further reading 1096 Microtubules, intermediate filaments, and actin filaments 110William V. DashekMicrotubules 110Intermediate filaments 113Actin filaments (microfilaments) 116References 119Further reading 1247 The mitochondrion 125Ray J. Rose, Terence W.‐Y. Tiew, and William V. DashekStructure and dynamics 125The mitochondrial genome 128Comparison of the mitochondrial genome with chloroplast and nuclear genomes 131The mitochondrial proteome and protein import 132Respiratory metabolite transporters 133The electron transport chain and oxidative phosphorylation 133The alternative electron transfer chain in plant mitochondria 139Plant mitochondria, stress responses and programmed cell death 139Other functions of plant mitochondria 140References 144Further reading 1458 Nucleus 146Yogesh Vikal and Dasmeet KaurStructural organization of the NE 147Nuclear pores 152The nucleolus 157Chromatin and chromosomes 165DNA structure 170DNA replication 173RNA structure, function, and synthesis 176Nucleocytoplasmic transport, nuclear import, and nuclear export 183The dynamics of NE biogenesis during mitosis 188The dynamics of nuclear pore complex biogenesis 196Cell cycle control 200Summary 205References 206Further reading 2079 Plant cell walls 209James E. Bidlack and William V. DashekIntroduction 209Structure 209Biosynthesis 216Chemical composition 217Biogenesis 222Function 225References 231Further reading 23810 Plastid structure and genomics 239Gurbachan S. MiglaniPlastid structure 239Different forms of plastids 240Plastid stromules 248Chlorophyll biosynthesis 248Plastid genomics 250Sequenced plastomes 253Promiscuous DNA 258Plastid genome organization 260Plastid gene organization, expression, and regulation 265Systems biology approach in understanding chloroplast development 269Chloroplast genetic engineering 284Recent trends in chloroplast research 289Summary 293References 294Further reading 29911 Photosynthesis 300J. Kenneth HooberIntroduction 300Evolution of photosynthesis 301Development of the chloroplast 310Absorption of light energy 317Generation of end products 324Distribution of the photosystems in thylakoid membranes 329Photoinhibition: damage and repair of the PS II reaction center 332Protection of PS II by carotenoids 332Incorporation of carbon as CO2 into carbohydrate 334End products of carbon assimilation 346Conclusions for the reactions of photosynthesis 348References 348Further reading 35012 Vacuoles and protein bodies 351William V. Dashek and Amy M. CloreVacuoles 351PBs and other protein storage compartments 359References 365Further reading 37013 Systems biology in plant cells and their organelles 371Rajdeep Kaur Grewal, Saptarshi Sinha, and Soumen RoySystems biology—“omics” 371Genomics 373Lipidomics 378Metabolomics 380Proteomics 382Transcriptomics 384Synthetic biology 386Acknowledgments 388References 389Further reading 391Appendix A 392Appendix B 400Appendix C 403Index 407

About the EditorsWilliam V. Dashek, Emeritus Professor, Mary Baldwin College, USA Dr. Dashek is the recipient of BS, MS and Ph.D. degree from Marquette University where he was a National Institute of Health pre-doctoral trainee. He was a post-doctorate fellow at the Michigan State University Plant research Laboratory. Subsequently, he began a lengthy Academic teaching and research career. Currently, Dashek is retired writing advanced textbooks. Gurbachan S. Miglani, Visiting Professor, School of Agricultural Biotechnology, Punjab Agricultural University, IndiaDr. Miglani obtained B.Sc. (Agri. & A.H.) and M.Sc. (Genetics) from Punjab Agricultural University (PAU), Ludhiana, Punjab, India and Ph.D. from Howard University, Washington, D.C. During his 35-year teaching stint at PAU he taught general and specialized courses in genetics. Even after retirement Miglani is still teaching molecular genetics and biotechnology at PAU. In addition to research and review papers, popular science articles, laboratory manuals he has published a dozen books and presently he is writing his next book.

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• Contributors ixPreface xiAcknowledgments xii1 An introduction to cells and their organelles 1William V. DashekCells 1Cell organelles – an introduction 6Ion channels 10Proton pumps 14Water channels 14Carriers 15Cell death 17References 18Further reading 242 Isolation and characterization of subcellular organelles from plant cells 25Milee Agarwal, P. Desai, and Harish PadhIsolation of subcellular organelles 26Identification and characterization of isolated organelles 33Summary 39References 39Further reading 413 Endoplasmic reticulum 42William V. DashekStructure 42Chemical composition 42Biogenesis 45Functions 45Posttranslational events 49Inhibitors 53In vitro protein synthesis 54Other functions 54References 54Further reading 604 The Golgi apparatus 61D. Davis, T.E. Wilkop, and Georgia DrakakakiThe Golgi apparatus 61Plant Golgi introduction 66Structure and organization 69Golgi‐mediated vesicular trafficking 71Plant Golgi‐dependent cellular processes 74Imaging and visualization 76Isolation and analysis 78Golgi genetics and genomics 81Significance 84Acknowledgment 85References 85Further reading 875 Microbodies 88Robert DonaldsonIntroducing peroxisomes 88Leaf peroxisomes 89Peroxisomes in oil seeds and pollen 91References 107Further reading 1096 Microtubules, intermediate filaments, and actin filaments 110William V. DashekMicrotubules 110Intermediate filaments 113Actin filaments (microfilaments) 116References 119Further reading 1247 The mitochondrion 125Ray J. Rose, Terence W.‐Y. Tiew, and William V. DashekStructure and dynamics 125The mitochondrial genome 128Comparison of the mitochondrial genome with chloroplast and nuclear genomes 131The mitochondrial proteome and protein import 132Respiratory metabolite transporters 133The electron transport chain and oxidative phosphorylation 133The alternative electron transfer chain in plant mitochondria 139Plant mitochondria, stress responses and programmed cell death 139Other functions of plant mitochondria 140References 144Further reading 1458 Nucleus 146Yogesh Vikal and Dasmeet KaurStructural organization of the NE 147Nuclear pores 152The nucleolus 157Chromatin and chromosomes 165DNA structure 170DNA replication 173RNA structure, function, and synthesis 176Nucleocytoplasmic transport, nuclear import, and nuclear export 183The dynamics of NE biogenesis during mitosis 188The dynamics of nuclear pore complex biogenesis 196Cell cycle control 200Summary 205References 206Further reading 2079 Plant cell walls 209James E. Bidlack and William V. DashekIntroduction 209Structure 209Biosynthesis 216Chemical composition 217Biogenesis 222Function 225References 231Further reading 23810 Plastid structure and genomics 239Gurbachan S. MiglaniPlastid structure 239Different forms of plastids 240Plastid stromules 248Chlorophyll biosynthesis 248Plastid genomics 250Sequenced plastomes 253Promiscuous DNA 258Plastid genome organization 260Plastid gene organization, expression, and regulation 265Systems biology approach in understanding chloroplast development 269Chloroplast genetic engineering 284Recent trends in chloroplast research 289Summary 293References 294Further reading 29911 Photosynthesis 300J. Kenneth HooberIntroduction 300Evolution of photosynthesis 301Development of the chloroplast 310Absorption of light energy 317Generation of end products 324Distribution of the photosystems in thylakoid membranes 329Photoinhibition: damage and repair of the PS II reaction center 332Protection of PS II by carotenoids 332Incorporation of carbon as CO2 into carbohydrate 334End products of carbon assimilation 346Conclusions for the reactions of photosynthesis 348References 348Further reading 35012 Vacuoles and protein bodies 351William V. Dashek and Amy M. CloreVacuoles 351PBs and other protein storage compartments 359References 365Further reading 37013 Systems biology in plant cells and their organelles 371Rajdeep Kaur Grewal, Saptarshi Sinha, and Soumen RoySystems biology—“omics” 371Genomics 373Lipidomics 378Metabolomics 380Proteomics 382Transcriptomics 384Synthetic biology 386Acknowledgments 388References 389Further reading 391Appendix A 392Appendix B 400Appendix C 403Index 407