Table of Contents: Preface 3.3.2. Eukaryotic chromosome structure Websites of Interest 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication Glossary 3.4.1. DNA replication is semiconservative 1. Introduction 3.4.2. DNA polymerases 1.1. What is a Gene? 3.4.3. Initiation of replication 1.2. What is a Genome? 3.4.4. DNA replication is semidiscontinuous 1.3. What is Genomic Biology? 3.4.5. DNA replication in Eukaryotes. 1.3.1. Structural Genomics 3.4.6. Replicating ends of chromosomes 1.3.2. Comparative Genomics 3.5. Transcription 1.3.3. Functional Genomics 3.5.1. Cellular RNAs are transcribed from DNA 1.4. Genomic Databases 3.5.2. RNA polymerases catalyze transcription 2. The beginnings of Genomic Biology – classical 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs genetics are produced from operons 2.1. Mendel & Darwin – traits are conditioned by genes 3.5.5. Beyond Operons – Modification of expression in 2.2. Genes are carried on chromosomes Prokaryotes 2.3. The chromosomal theory of inheritance 3.5.6. Transcriptions in Eukaryotes 2.4. Additional Complexity of Mendelian Inheritance 3.5.7. Processing primary transcripts into mature mRNA 2.4.1. Multiple alleles 3.6. Translation 2.4.2. Incomplete dominance and co-dominance 3.6.1. The Nature of Proteins 2.4.3. Sex linked inheritance 2.4.4. Epistasis 3.6.2. The Genetic Code 2.4.5. Epigenetics 3.6.3. tRNA – The decoding molecule 2.5. The Law of Independent Assortment 3.6.4. Peptides are synthesized on Ribosomes 2.5.1. Meiosis: chromosomes assort independently 3.6.5. Translation initiation, elongation, and termnation 2.5.2. Mapping genes on chromosomes 3.6.6. Protein Sorting in Eukaryotes 2.6. Quantitative Genetics: Traits that are Continuously Variable 4. Genomic Biologists tool kit 2.7. Population Genetics: Traits in groups of individuals 4.1. Restriction Endonucleases – making “sticky ends” 3. The beginnings of Genomic Biology – molecular 4.2. Cloning Vectors genetics 4.2.1. Simple Cloning Vectors 3.1. DNA is the Genetic Material 4.2.2. Expression Vectors 3.2. Watson & Crick – The structure of DNA 4.2.3. Shuttle Vectors 3.3. Chromosome structure 4.2.4. Phage Vectors 3.3.1. Prokaryotic chromosome structure 4.2.5. Artificial Chromosome Vectors CONCEPTS OF GENOMIC BIOLOGY Page 1 4.3. Methods for Sequence Amplification • Microarray 4.3.1. Polymerase Chain Reaction 7.10. The Proteome 4.3.2. Cloning Recombinant DNA 7.11. The Metabolome 4.3.3. Cloning DNA in Expression Vectors 8. Genomic Applications 4.3.4. Making complementary DNA (cDNA) 8.4. Human biology 4.4. Methods for Sequence Amplification - Cont. 8.5. The Environment 4.4.5. Cloning a cDNA Library 8.6. Food & fiber production 4.5. Genomic Libraries 8.7. Evolutionary biology 4.6. DNA separation – electrophoresis Epilogue 4.7. DNA sequence identification – DNA hybridization

5. Structural Genomics 5.4. Sequencing DNA molecules • Sanger sequencing – dideoxy sequencing • Automated capillary DNA sequencing robots • Next generation sequencing – pyrosequencing 5.5. Genomic sequence libraries 5.6. Map-based strategies – molecular polymorphisms 5.7. Whole genome shotgun sequencing 5.8. Bioinformatics and gene identification 5.9. About sequenced genomes 6. Comparative Genomics 6.4. Genomic variation – mutations 6.5. Genomic variation – polymorphisms 6.6. Phylogenetic trees 6.7. The tree of life 7. Functional Genomics – Overview 7.4. Identification of protein structure and function 7.5. Non-protein-coding genes 7.6. Gene expression – Prokaryotes 7.7. Gene expression – Eukaryotes 7.8. Gene expression – Signal Transduction 7.9. The transcriptome – Measuring gene expression • Northern blot • RT-PCR • Quantitative PCR CONCEPTS OF GENOMIC BIOLOGY Page 2 (Celera Corporation, which was formally launched in 1998. The dynamics and interaction of these 2 efforts is an interesting PREFACE (RETURN) study on how we identify and fund science today, and how Prior to about 1990 few people conceived of the idea of a public sector research is both in competition with and genome, much less undertaken the investigation of such. collaboration with privately funded corporate research. This is However in 1990 the Human Genome Project (HGP) was such an interesting plethora of information that several books initiated as an international scientific research collaboration have been written describing the HCP and Celera Genomics with the goals of: 1) determining the sequence of nucleotide efforts. A couple of these are given in the book list below: bases that make up a haploid copy of human chromosomes; 2) identifying all of the genes of the human genome both physically and functionally; and 3) mapping all of the genes identified to specific human chromosomes. The HGP remains the world's largest collaborative biological project. The project was proposed and funded by the US government through the National Instutues of Health (NIH). Planning started in 1984, and the project got underway in 1990. In 2003 President Bill Clinton declared the HGP a rousing success and essentially complete with the production of a first draft of the This eBook is intended to provide knowledge of the technology, achievements, and ongoing activities of what started as the HGP, but now human genome. In fact, work on gene identification, mapping, involves much broader considerations that are shaping the future of the and function is ongoing even today, and has yielded a treasure study of biology. In order to appreciate this information and to make it trove of knowledge about the human genome as well as the maximally useful, a brief synopsis of important concepts from classical and genes and genomes of many other microbes, fungi, plants and molecular genetics is presented. This followed by an analysis of the animals along the way that is revolutionizing not only health technology used by genomic biologists, and a summary of the significant science-related research but virtually every aspect of findings in DNA sequencing (structural genomics), sequence comparisons of a wide range of organism (comparative genomics), and information on contemporary biology. how genes in genomes produce their phenotype (functional genomics). The publicly funded project was led, by Dr. Francis Collins and involved more than in twenty universities and research Bob Locy, December, 2014 centers in the United States, the United Kingdom, Japan, France, Germany, and China. A parallel project was conducted in the private sector led by Dr. Craig Venter of the Celera Genomics CONCEPTS OF GENOMIC BIOLOGY Page 3

 Websites of interest (Return) General EMBL (European Bioinformatics Institute) Gennome News Network Human Genome Project (HGP) National Center for Bioltechnology Information (NCBI) Tree of Life Web Project Genome Databases CAMERA Resource for microbial genomics and metagenomics Corn the Maize Genetics and Genomics Database EcoCyc E. coli K-12 database PATRIC, the PathoSystems Resource Integration Center Flybase Drosophila melanogaster genome JGI Genomes of the DOE-Joint Genome Institute Mouse Genome Database (MGI) National Microbial Pathogen Data Resource. Repbase database for repetitive elements (transposons). Saccharomyces Genome Database (yeast) Xenbase genome of Xenopus tropicalis and Xenopus laevis Wormbase Caenorhabditis elegans database Zebrafish Information Network TAIR The Arabidopsis Information Resource Rat Genome Database (RGD) Banana Genome Hub Bacterrial Small Regulatory RNA Database

CONCEPTS OF GENOMIC BIOLOGY Page 4  Glossary (Return)